├── .gitattributes ├── .gitignore ├── .travis.yml ├── CONTRIBUTING ├── Dockerfile ├── LICENSE.txt ├── README.md ├── chunks ├── 10xgenomics-2019-07-09.txt ├── Mice_TCRs_specific_to_B16_melanoma_neoantigens_(Shagina_et_al_2024).txt ├── PDB_Database.txt ├── PMID_10756006.txt ├── PMID_10925283.txt ├── PMID_11046006.txt ├── PMID_11756174.txt ├── PMID_11930311.txt ├── PMID_12165524.txt ├── PMID_12466894.txt ├── PMID_12504586.txt ├── PMID_12555663.txt ├── PMID_15589168.txt ├── PMID_15596521.txt ├── PMID_15753288.txt ├── PMID_15849183.txt ├── PMID_16148129.txt ├── PMID_16237109.txt ├── PMID_16287711.txt ├── PMID_16326979.txt ├── PMID_16772368.txt ├── PMID_16982909.txt ├── PMID_17082594.txt ├── PMID_17121793.txt ├── PMID_17287271.txt ├── PMID_17459926.txt ├── PMID_17709536.txt ├── PMID_17893201.txt ├── PMID_18270323.txt ├── PMID_18802118.txt ├── PMID_19014475.txt ├── PMID_19017975.txt ├── PMID_19349463.txt ├── PMID_19776383.txt ├── PMID_19864595.txt ├── PMID_20139278.txt ├── PMID_20432235.txt ├── PMID_21118816.txt ├── PMID_21135165.txt ├── PMID_21160049.txt ├── PMID_21555537.txt ├── PMID_21562156.txt ├── PMID_21752903.txt ├── PMID_22044339.txt ├── PMID_22210916.txt ├── PMID_22278241.txt ├── PMID_22314361.txt ├── PMID_22323539.txt ├── PMID_23028307.txt ├── PMID_23267020.txt ├── PMID_23521884.txt ├── PMID_23637823.txt ├── PMID_23933763.txt ├── PMID_24069285.txt ├── PMID_24512815.txt ├── PMID_24600035.txt ├── PMID_24711416.txt ├── PMID_24906112.txt ├── PMID_25157096.txt ├── PMID_25320304.txt ├── PMID_25339770.txt ├── PMID_25609818.txt ├── PMID_25801351.txt ├── PMID_25837513.txt ├── PMID_25911754.txt ├── PMID_25925682.txt ├── PMID_26860370.txt ├── PMID_27111229.txt ├── PMID_27252176.txt ├── PMID_27645996.txt ├── PMID_27760342.txt ├── PMID_28103239.txt ├── PMID_28146579.txt ├── PMID_28250417.txt ├── PMID_28423320.txt ├── PMID_28623251.txt ├── PMID_2862975.txt ├── PMID_28636589.txt ├── PMID_28636592.txt ├── PMID_28724766.txt ├── PMID_28934479.txt ├── PMID_28945243.txt ├── PMID_28975614.txt ├── PMID_28993513.txt ├── PMID_29150238.txt ├── PMID_29275860.txt ├── PMID_29429978.txt ├── PMID_29483360.txt ├── PMID_29483513.txt ├── PMID_29752423.txt ├── PMID_29997621.txt ├── PMID_30487790.txt ├── PMID_30587531.txt ├── PMID_33927715.txt ├── PMID_33945786.txt ├── PMID_34433824.txt ├── PMID_34793243.txt ├── PMID_34811538.txt ├── PMID_34880106.txt ├── PMID_35314848.txt ├── PMID_35525797.txt ├── PMID_35687696.txt ├── PMID_35750048.txt ├── PMID_35990517.txt ├── PMID_36477533.txt ├── PMID_37280206.txt ├── PMID_37418020.txt ├── PMID_38439958.txt ├── PMID_38508137.txt ├── PMID_38737448.txt ├── PMID_38866784.txt ├── PMID_38898278.txt ├── PMID_39043656.txt ├── PMID_39074636.txt ├── PMID_39286976 .txt ├── PMID_7807026.txt ├── PMID_9207000.txt ├── PMID_9560256.txt ├── PMID_9862375.txt ├── PMID_9971792.txt ├── attaf-etal-2020-04-07.txt ├── bunkofske-etal-2024.txt ├── covid19-2020-05-19.txt ├── covid19-heathlab-26-11-2021.txt ├── covid19-sewell-13-05-2021.txt ├── drlcook-etal-2020-02-01.txt ├── efimovlab-2021-09-15_LTI_VDJdb.txt ├── evgeny-etal-2018-04.txt ├── goncharov-gluten-2023-05-06.txt ├── goncharov-sarscov2-mhcii-2021-08-12.txt ├── goncharov-taa-2020-10-12.txt ├── goncharov-taa-2020-11-02.txt ├── goncharov-taa-2020-11-24.txt ├── goncharov-taa-2021-02-01.txt ├── goncharov-taa-2021-08-12.txt ├── goncharov-taa-2022-01-27.txt ├── goncharov-various-2023-04-18.txt ├── goncharov-various-2023-05-06.txt ├── greenshields_cole_2019.txt ├── hayleymc-2023-08-13.txt ├── huang-etal-2020-01-09.txt ├── kedzierska-etal-2021-06-18.txt ├── luciani-samir-etal-hcv-14-09-2021.txt ├── menon_etal_2024.txt ├── nguyen-etal-2023.txt ├── paley-etal-2024-06-18.txt ├── rius-etal-2019-07-05.txt ├── sewell-etal-2017-04-13.txt ├── smith-etal-2019-10-30.txt ├── thomas_etal_30-07-21.txt └── vandesandt-etal-2019-11-04.txt ├── chunks_unformatted └── Mice_TCRs_specific_to_B16_melanoma_neoantigens_(Shagina_et_al_2024).txt ├── database └── dummy ├── images └── vdjdb-splash.png ├── latest-version.txt ├── patches ├── antigen_epitope_species_gene.dict └── nomenclature.conversions ├── release.sh ├── release_docker.sh ├── res ├── segments.aaparts.txt └── segments.txt ├── src ├── AlignBestSegments.py ├── BuildDatabase.groovy ├── Cdr3Fixer.groovy ├── FixType.groovy ├── FixerResult.groovy ├── KmerScanner.groovy ├── LICENSE ├── OneSideFixerResult.groovy ├── README.md ├── SearchResult.groovy ├── SlimComplexAccumulator.groovy ├── Table.groovy ├── Util.groovy └── VdjdbScoreFactory.groovy ├── summary ├── MakeEmbedableHtml.groovy └── vdjdb_summary.Rmd ├── template.xls ├── test.sh └── withheld ├── PMID_18799721.txt ├── PMID_19542443.txt ├── PMID_27254288.txt ├── PMID_7964506.txt └── PMID_9971792.txt /.gitattributes: -------------------------------------------------------------------------------- 1 | README.md linguist-documentation -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | tmp/ 2 | database/ 3 | !database/dummy 4 | 5 | ## Groovy / Java 6 | 7 | *.class 8 | target/ 9 | .idea/ 10 | *.iml 11 | dependency-reduced-pom.xml 12 | 13 | ## Python 14 | 15 | # Byte-compiled / optimized / DLL files 16 | __pycache__/ 17 | *.py[cod] 18 | *$py.class 19 | 20 | # C extensions 21 | *.so 22 | 23 | # Distribution / packaging 24 | .Python 25 | env/ 26 | build/ 27 | develop-eggs/ 28 | dist/ 29 | downloads/ 30 | eggs/ 31 | .eggs/ 32 | lib/ 33 | lib64/ 34 | parts/ 35 | sdist/ 36 | var/ 37 | *.egg-info/ 38 | .installed.cfg 39 | *.egg 40 | 41 | # PyInstaller 42 | # Usually these files are written by a python script from a template 43 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 44 | *.manifest 45 | *.spec 46 | 47 | # Installer logs 48 | pip-log.txt 49 | pip-delete-this-directory.txt 50 | 51 | # Unit test / coverage reports 52 | htmlcov/ 53 | .tox/ 54 | .coverage 55 | .coverage.* 56 | .cache 57 | nosetests.xml 58 | coverage.xml 59 | *.cover 60 | .hypothesis/ 61 | 62 | # Translations 63 | *.mo 64 | *.pot 65 | 66 | # Django stuff: 67 | *.log 68 | 69 | # Sphinx documentation 70 | docs/_build/ 71 | 72 | # PyBuilder 73 | target/ 74 | 75 | ## R 76 | .Rhistory 77 | .DS_Store 78 | .RData 79 | 80 | ## Linux 81 | .directory 82 | 83 | ## motifs 84 | vdjdb-motifs 85 | 86 | ## output 87 | output 88 | 89 | summary/*.pdf 90 | summary/*.html 91 | summary/*.txt 92 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | dist: xenial 2 | 3 | language: 4 | - groovy 5 | - python 6 | 7 | python: 8 | - 2.7 9 | 10 | jdk: 11 | - openjdk8 12 | 13 | before_install: 14 | - sudo pip install pandas 15 | - sudo pip install 'biopython==1.76' 16 | 17 | script: 18 | - cd src/ 19 | - travis_wait groovy -cp . BuildDatabase.groovy --no2fix 20 | -------------------------------------------------------------------------------- /CONTRIBUTING: -------------------------------------------------------------------------------- 1 | **IMPORTANT** 2 | The issue tracker and pull requests are designed for working 3 | (depositing, updating and proofreading) with raw VDJdb data. 4 | For issues related to vdjdb.cdr3.net, please use the corresponding 5 | issue tracker: https://github.com/antigenomics/vdjdb-web/issues 6 | 7 | Please follow the instructions specified in README.md file in 8 | the root folder of this repository when preparing your submissions. 9 | If you have any questions regarding data submission, either post 10 | an issue here or mail me to `mikhail dоt shugay аt gmail dоt com` 11 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | FROM ubuntu:18.04 2 | 3 | # Fix certificate issues 4 | RUN apt-get update && \ 5 | apt-get install -y ca-certificates-java && \ 6 | apt-get clean && \ 7 | update-ca-certificates -f; 8 | 9 | # `openjdk-8` 10 | RUN apt-get update 11 | RUN apt-get install -y --no-install-recommends software-properties-common 12 | RUN add-apt-repository -y ppa:openjdk-r/ppa 13 | RUN apt-get update 14 | 15 | RUN apt-get update 16 | RUN add-apt-repository -y universe 17 | RUN apt-get update 18 | RUN apt-get install -y python python-pip 19 | 20 | RUN pip install 'pandas==0.24.2' 'numpy==1.16.6' 21 | RUN pip install 'biopython==1.76' 22 | 23 | RUN apt-get install -y openjdk-8-jre openjdk-8-jdk openjdk-8-jdk-headless openjdk-8-jre-headless 24 | RUN update-alternatives --config java 25 | RUN update-alternatives --config javac 26 | 27 | # Setup JAVA_HOME -- useful for docker commandline 28 | ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64/ 29 | RUN export JAVA_HOME 30 | 31 | RUN apt-get install -y wget 32 | RUN apt-get install -y unzip 33 | RUN apt-get install -y git 34 | RUN apt-get install -y curl 35 | RUN apt-get install -y zip 36 | RUN apt-get install -y pandoc 37 | 38 | SHELL ["/bin/bash", "-c"] 39 | 40 | RUN curl -s "https://get.sdkman.io" | bash 41 | RUN source "$HOME/.sdkman/bin/sdkman-init.sh" && \ 42 | sdk install groovy 3.0.9 43 | 44 | # needed for R 45 | ENV DEBIAN_FRONTEND noninteractive 46 | 47 | RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 48 | RUN add-apt-repository -y 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/' 49 | RUN apt-get update 50 | 51 | RUN apt-get update \ 52 | && apt-get install -y --no-install-recommends \ 53 | r-base \ 54 | r-base-dev \ 55 | r-recommended 56 | 57 | # for R deps 58 | RUN apt-get install -y libnlopt-dev 59 | RUN apt-get install -y libfontconfig1-dev 60 | RUN apt-get install -y libcurl4-openssl-dev 61 | RUN apt-get install -y libssl-dev 62 | RUN apt-get install -y libxml2 libxml2-dev 63 | RUN apt-get install -y libcairo2-dev libxt-dev libx11-dev 64 | RUN apt-get install -y libmagick++-dev 65 | RUN apt-get install -y libharfbuzz-dev libfribidi-dev 66 | 67 | # 'knitr', 'htmltools', 'jquerylib', 'stringr' are not available for package 'rmarkdown' 68 | RUN Rscript -e 'install.packages(c("knitr", "ggplot2", "RColorBrewer", "data.table", "forcats", "ggh4x", "ggalluvial", "circlize", "ggrepel", "tidyverse", "httr", "xml2", "stringr", "gridExtra", "maps", "scatterpie", "dplyr", "stringr", "stringdist", "reshape2", "igraph", "ggseqlogo", "parallel", "cowplot"))' 69 | 70 | RUN apt-get install -y texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra 71 | RUN apt-get install -y build-essential procps curl file git 72 | 73 | RUN wget https://github.com/mikessh/vdjtools/releases/download/1.2.1/vdjtools-1.2.1.zip 74 | RUN mkdir -p /software/bin/ 75 | RUN unzip vdjtools-1.2.1.zip 76 | RUN cp -r vdjtools-1.2.1/* /software/bin/ 77 | RUN chmod +x /software/bin/vdjtools 78 | 79 | ENV PATH="/usr/lib/jvm/java-8-openjdk-amd64/bin:${PATH}" 80 | ENV PATH="/software/bin:${PATH}" 81 | 82 | RUN touch docker.sh 83 | RUN echo '# /bin/sh' >> docker.sh 84 | RUN echo '[[ -s "$HOME/.sdkman/bin/sdkman-init.sh" ]] && source "$HOME/.sdkman/bin/sdkman-init.sh"' >> docker.sh 85 | RUN echo 'mkdir -p vcs' >> docker.sh 86 | RUN echo 'cd vcs' >> docker.sh 87 | RUN echo 'echo $(pwd)' >> docker.sh 88 | RUN echo 'git clone https://github.com/antigenomics/vdjdb-db vdjdb-db' >> docker.sh 89 | RUN echo 'git clone https://github.com/antigenomics/vdjdb-motifs vdjdb-motifs' >> docker.sh 90 | RUN echo 'cd vdjdb-db' >> docker.sh 91 | RUN echo 'echo $(pwd)' >> docker.sh 92 | RUN echo 'mkdir -p /root/output' >> docker.sh 93 | RUN echo 'bash release.sh 2>&1 | tee /root/output/buildlog' >> docker.sh 94 | RUN echo 'cp -r database/*zip /root/output/' >> docker.sh 95 | 96 | CMD [ "bash", "docker.sh" ] -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/antigenomics/vdjdb-db/4fe22b7969d0ab8c6910bbdce51c06f1f33679ea/LICENSE.txt -------------------------------------------------------------------------------- /chunks/PMID_10756006.txt: -------------------------------------------------------------------------------- 1 | cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id submitter method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id comment 2 | CASSVDGTGGALGNTIYF TRBV9 TRBJ1-3 HomoSapiens HLA-A*02:01 B2M MHCI YILEETSVM IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 1/22 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw12 putative original V-segment nomenclature is Wei et al., 1994 3 | CAWSWGDSTNSPLHF TRBV29-1 TRBJ1-6 HomoSapiens HLA-A*02:01 B2M MHCI YILEETSVM IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 19/22 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw14 V-segment in the article - Vβ210S1, IMGT analogue is not identified, putative original V-segment nomenclature is Wei et al., 1994 4 | CASSLVGGTGSVSYQFF TRBV11-2 TRBJ2-1 HomoSapiens HLA-A*02:01 B2M MHCI YILEETSVM IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 1/22 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw15 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 5 | CASSLLMATNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*18 B2M MHCI ELKRKMIYM IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 1/21 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw16 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 6 | CASSYRANYEQYF TRBV7-9 TRBJ2-7 HomoSapiens HLA-B*18 B2M MHCI ELKRKMIYM IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 2/21 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw17 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 7 | CASSQAVASGGGRSEQFF TRBV3-2 TRBJ2-1 HomoSapiens HLA-B*18 B2M MHCI ELKRKMIYM IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 1/21 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw18 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 8 | CASVTGSTDTQYF TRBV2 TRBJ2-3 HomoSapiens HLA-B*18 B2M MHCI ELKRKMIYM IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 7/21 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw19 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 9 | CASSDGTAYEQYF TRBV2 TRBJ2-7 HomoSapiens HLA-B*18 B2M MHCI ELKRKMIYM IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 10/21 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw20 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 10 | CASSLARNQPQHF TRBV4-1 TRBJ1-5 HomoSapiens HLA-B*18 B2M MHCI CVETMCNEY IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 1/2 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw21 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 11 | CASGGADMKTEAFF TRBV19 TRBJ1-1 HomoSapiens HLA-B*18 B2M MHCI CVETMCNEY IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 1/2 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw22 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 12 | CSANPDWGLQLWLHLRF TRBV20-1 TRBJ2-1 HomoSapiens HLA-B*18 B2M MHCI DEEDAIAAY IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 1/2 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw23 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 13 | CASSPGGGKETQYF TRBV7-6 TRBJ2-5 HomoSapiens HLA-B*18 B2M MHCI DEEDAIAAY IE1 CMV PMID:10756006 Anastasiia Sycheva antigen-loaded-targets,cloning-by-limiting-dilution 1/2 sanger CD8+ healthy, CMV-seropositive donor C PBMC A2,A25,B18,B44,Cw5,Cw24 see the article for details, putative original V-segment nomenclature is Wei et al., 1994 14 | -------------------------------------------------------------------------------- /chunks/PMID_11756174.txt: -------------------------------------------------------------------------------- 1 | cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id submitter method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id comment 2 | CASSLAPGTTNEKLFF TRBV7-3*01 TRBJ1-4*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:11756174 Anastasiia Sycheva tetramer-sort sanger CD8+ healthy, CMV-seropositive Donor 01 PBMC HLA-A*02:01 and/or HLA-B*07:02 BV6.1 = TRBV 6S1 (Wei et al.), sequence of isolated spectratyping peak 3 | CASSLVASGQETQYF TRBV7-3*01 TRBJ2-5*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:11756174 Anastasiia Sycheva tetramer-sort sanger CD8+ healthy, CMV-seropositive Donor 02 PBMC HLA-A*02:01 and/or HLA-B*07:02 BV6.1 = TRBV 6S1 (Wei et al.), sequence of isolated spectratyping peak 4 | CASSLQAGANEQFF TRBV7-3*01 TRBJ2-1*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:11756174 Anastasiia Sycheva tetramer-sort sanger CD8+ healthy, CMV-seropositive Donor 02 PBMC HLA-A*02:01 and/or HLA-B*07:02 BV6.1 = TRBV 6S1 (Wei et al.), sequence of isolated spectratyping peak 5 | CASSLSGGGEQFF TRBV7-3*01 TRBJ2-1*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:11756174 Anastasiia Sycheva tetramer-sort sanger CD8+ healthy, CMV-seropositive Donor 02 PBMC HLA-A*02:01 and/or HLA-B*07:02 BV6.1 = TRBV 6S1 (Wei et al.), sequence of isolated spectratyping peak 6 | CASSDGIQGAWANVLTF TRBV24-1*01 TRBJ2-6*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:11756174 Anastasiia Sycheva tetramer-sort sanger CD8+ healthy, CMV-seropositive Donor 02 PBMC HLA-A*02:01 and/or HLA-B*07:02 BV15 = TRBV 15S1 (Wei et al.), there is mismatch in TRBJ, sequence of isolated spectratyping peak 7 | -------------------------------------------------------------------------------- /chunks/PMID_11930311.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSESTGTAYGYTF TRBV13-1 TRBJ1-2 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:11930311 tetramer-sort 60% 002 3 | 2 CASSLGNYEQYF TRBV14 TRBJ2-7 HomoSapiens HLA-A*02 B2M MHCI VLEETSVML IE1 CMV PMID:11930311 tetramer-sort 76% 014 4 | 3 CASSLSTGGALGTIYF TRBV1 TRBJ1-3 HomoSapiens HLA-A*02 B2M MHCI VLEETSVML IE1 CMV PMID:11930311 tetramer-sort 42% 015 5 | 4 CASSLTSGGPDTQYF TRBV14 TRBJ2-3 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:11930311 tetramer-sort 75% 010 6 | 5 CASSWDSQSSGNSIYF TRBV5-1 TRBJ1-3 HomoSapiens HLA-A*02 B2M MHCI VLEETSVML IE1 CMV PMID:11930311 tetramer-sort 24% 014 7 | 6 CASSWDSQSSGNSIYF TRBV5-1 TRBJ1-3 HomoSapiens HLA-A*02 B2M MHCI VLEETSVML IE1 CMV PMID:11930311 tetramer-sort 93% 004 8 | 7 CSVSEGASEQYF TRBV4 TRBJ2-7 HomoSapiens HLA-A*02 B2M MHCI VLEETSVML IE1 CMV PMID:11930311 tetramer-sort 99% 002 9 | 8 CASSWDSQSSGNSIYF TRBV5-1 TRBJ1-3 HomoSapiens HLA-A*02 B2M MHCI VLEETSVML IE1 CMV PMID:11930311 tetramer-sort 7% 015 10 | -------------------------------------------------------------------------------- /chunks/PMID_12165524.txt: -------------------------------------------------------------------------------- 1 | cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id submitter method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id comment 2 | CASSPQTGTGGYGYTF TRBV6-5 TRBJ1.2 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.085 healthy, CMV-seropositive 001 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV13.1 3 | CASSPQTGTGGYGYTF TRBV6-5 TRBJ1.2 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.07 healthy, CMV-seropositive 002 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV13.1 4 | CASSPLFGTSGGETYYF TRBV6-5 TRBJ2.5 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.07 healthy, CMV-seropositive 002 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV13.1 5 | CASSPQTGTGGYGYTF TRBV6-5 TRBJ1.2 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.024 healthy, CMV-seropositive 004 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV13.1 6 | CASSPQTGASYGYTF TRBV6-5 TRBJ1.2 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.024 healthy, CMV-seropositive 004 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV13.1 7 | CASSLVGGRYGYTF TRBV12-3 TRBJ1.2 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.024 healthy, CMV-seropositive 004 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV8 8 | CASSPQTGTGGYGYTF TRBV6-5 TRBJ1.2 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.017 healthy, CMV-seropositive 005 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV13.1 9 | CASSPATGTIYGYTF TRBV6-5 TRBJ1.2 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.017 healthy, CMV-seropositive 005 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV13.1 10 | CASSLTSGSPDTQYF TRBV27 TRBJ2.3 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.017 healthy, CMV-seropositive 005 PBMC HLA-A2 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV14 11 | CASSILGVSSYNEQFF TRBV7-6 TRBJ2.1 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.23 healthy, CMV-seropositive 025 PBMC HLA-A2, HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV6.4 12 | CASSFRDYGRYEQYF TRBV7-6 TRBJ2.7 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.038 healthy, CMV-seropositive 027 PBMC HLA-A2, HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV6.4 13 | CASSILGISSYNEQFF TRBV7-6 TRBJ2.1 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.036 healthy, CMV-seropositive 029 PBMC HLA-A2/HLA-A2, HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV6.4 14 | CASSLGPITEAPF TRBV27 TRBJ1.1 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.059 healthy, CMV-seropositive 030 PBMC HLA-A2, HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV14 15 | CASSPSAQYNEQFF TRBV7-6 TRBJ2.1 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.065 healthy, CMV-seropositive 040 PBMC HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV6.4 16 | CASSLRGAATDTQYF TRBV7-6 TRBJ2.1 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.065 healthy, CMV-seropositive 040 PBMC HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV6.4 17 | CASTNHDRGGMNTEAPF TRBV7-6 TRBJ1.1 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.073 healthy, CMV-seropositive 041 PBMC HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV6.4 18 | CASSLVGQGLSDEQFF TRBV7-6 TRBJ2.1 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.035 healthy, CMV-seropositive 043 PBMC HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: BV6.4 19 | CATVLRMDSSYKLIF TRAV3 TRAJ16.5 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.23 healthy, CMV-seropositive 025 PBMC HLA-A2, HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: AV3.1 20 | CAVRVSMDSSYKLIF TRAV16 TRAJ16.5 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.065 healthy, CMV-seropositive 040 PBMC HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: AV16.1 21 | CAMREGRDSSYKLIF TRAV6 TRAJ16.5 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.073 healthy, CMV-seropositive 041 PBMC HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: AV6.1 22 | CAVRVSMDSSYKLIF TRAV16 TRAJ16.5 HomoSapiens HLA-B*07:02 B2M MHCI TPRVTGGGAM pp65 CMV PMID:12165524 Ivan Zvyagin tetramer-magnetic-selection sanger CD8 0.073 healthy, CMV-seropositive 041 PBMC HLA-B7 Ab, PCR Ambiguous TRBV nomenclature used. V segment name originally provided in the paper: AV16 23 | -------------------------------------------------------------------------------- /chunks/PMID_15596521.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CIVRAPGRADMR TRAV26-1 TRAJ43 CASSYLPGQGDHYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEKGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 005 PBMC HLA-A*02:01,HLA-A*24:02;HLA-B*08:01,HLA-B*5701;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*07:01,HLA-DRB*13:01 3 | 2 CASSFEAGQGFFSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEKGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 065 PBMC HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 4 | 3 CAVPSGAGSYQLT TRAV23 TRAJ28 CASSFEPGQGFYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEKGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 200 PBMC HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01 5 | 4 CAVKASGSRLT TRAV2-1 TRAJ58 CASSYEPGQVSHYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEKGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 046 PBMC HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 6 | 5 CAYRPPGTYKYI TRAV14-1 TRAJ40 CASSALASLNEQF TRBV14 TRBJ2-1 HomoSapiens HLA-B*08 B2M MHCI FLKEKGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 046 PBMC HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 7 | 6 CIVRAPGRADMR TRAV26-1 TRAJ43 CASSYLPGQGDHYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEQGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 005 TCL culture HLA-A*02:01,HLA-A*24:02;HLA-B*08:01,HLA-B*5701;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*07:01,HLA-DRB*13:01 8 | 7 CASSFEAGQGFFSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEQGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 065 TCL culture HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 9 | 8 CAVPSGAGSYQLT TRAV23 TRAJ28 CASSFEPGQGFYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEQGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 200 TCL culture HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01 10 | 9 CAVKASGSRLT TRAV2-1 TRAJ58 CASSYEPGQVSHYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEQGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 046 TCL culture HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 11 | 10 CIVRAPGRADMR TRAV26-1 TRAJ43 CASSYLPGQGDHYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKETGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 005 TCL culture HLA-A*02:01,HLA-A*24:02;HLA-B*08:01,HLA-B*5701;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*07:01,HLA-DRB*13:01 12 | 11 CASSFEAGQGFFSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKETGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 065 TCL culture HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 13 | 12 CAVPSGAGSYQLT TRAV23 TRAJ28 CASSFEPGQGFYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKETGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 200 TCL culture HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01 14 | 13 CAVKASGSRLT TRAV2-1 TRAJ58 CASSYEPGQVSHYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKETGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 046 TCL culture HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 15 | 14 CIVRAPGRADMR TRAV26-1 TRAJ43 CASSYLPGQGDHYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEMGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 005 TCL culture HLA-A*02:01,HLA-A*24:02;HLA-B*08:01,HLA-B*5701;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*07:01,HLA-DRB*13:01 16 | 15 CASSFEAGQGFFSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEMGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 065 TCL culture HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 17 | 16 CAVPSGAGSYQLT TRAV23 TRAJ28 CASSFEPGQGFYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEMGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 200 TCL culture HLA-A*02,HLA-A*24:02;HLA-B*08:01,HLA-B*15;HLA-Cw*07,HLA-Cw*12;HLA-DRB*13:01,HLA-DRB*03:01 18 | 17 CAVKASGSRLT TRAV2-1 TRAJ58 CASSYEPGQVSHYSNQPQH TRBV13-2 TRBJ1-5 HomoSapiens HLA-B*08 B2M MHCI FLKEMGGL Nef HIV-1 PMID:15596521 tetramer-sort sanger antigen-loaded-targets CD8+ HIV+ 046 TCL culture HLA-A*01:01,HLA-A*02:01;HLA-B*08:01,HLA-B*57:01;HLA-Cw*06:02,HLA-Cw*07:01;HLA-DRB*08:03:2,HLA-DRB*15:01:1 19 | -------------------------------------------------------------------------------- /chunks/PMID_15753288.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSLLVSGNEQF TRBV21 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 62% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 3 | 2 CASSTRQNTEAF TRBV3 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 7% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 4 | 3 CASSQGVGNTIY TRBV7 TRBJ1-3 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 6% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 5 | 4 CASSRYQTEAF TRBV3 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 5% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 6 | 5 CASSGMRGTEAFF TRBV7 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 6% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 7 | 6 CSARDLAEGTYEQY TRBV2 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 5% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 8 | 7 CASSLDVGEQY TRBV6-4 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 4% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 9 | 8 CASSLKAAAYNEQF TRBV5 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 2% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 10 | 9 CASSPALTDRLAYFSYNEQF TRBV1 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 2% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 11 | 10 CSAISGTSGIFSYNEQF TRBV2 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 12 | 11 CAIGGNTEAF TRBV12-1 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 vCP205 KK10 PBMC 13 | 12 CASSLLVSGNEQF TRBV21 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 38% sanger CD8+ vaccinated,infected 202-T07 acute KK10 PBMC 14 | 13 CASSSGMRGTEAF TRBV7 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 29% sanger CD8+ vaccinated,infected 202-T07 acute KK10 PBMC 15 | 14 CASSLDVGEQY TRBV6-4 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 20% sanger CD8+ vaccinated,infected 202-T07 acute KK10 PBMC 16 | 15 CASSLGVNAVEQY TRBV7 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 8% sanger CD8+ vaccinated,infected 202-T07 acute KK10 PBMC 17 | 16 CSARDLAEGTYEQY TRBV2 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 5% sanger CD8+ vaccinated,infected 202-T07 acute KK10 PBMC 18 | 17 CASGQSGTAYNEQF TRBV10 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 38% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 19 | 18 CSARVGLNNEQF TRBV2 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 23% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 20 | 19 CASSLLVSGNEQF TRBV21 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 7% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 21 | 20 CSARAPAGMYPGNQP TRBV2 TRBJ1-5 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 6% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 22 | 21 CASSSGMRGTEAF TRBV7 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 6% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 23 | 22 CASSQGQYGNTIYF TRBV7 TRBJ1-3 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 3% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 24 | 23 CASSQGRLDNGQY TRBV7 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 3% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 25 | 24 CASSTRGNTEAF TRBV3 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 3% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 26 | 25 CASSLGVNAVEQY TRBV7 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 3% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 27 | 26 CASSQGRWGTEAF TRBV7 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 28 | 27 CASSLGANAVEQY TRBV7 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 29 | 28 CASSSGLAGGREQF TRBV7 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 30 | 29 CASSRYQTEAF TRBV3 TRBJ1-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 31 | 30 CASSPGTFHNEQF TRBV7 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 32 | 31 CASSDPTGSGAYEQY TRBV21 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 33 | 32 CASGQSGTACNEQF TRBV10 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 1% sanger CD8+ vaccinated,infected 202-T07 chronic KK10 PBMC 34 | 33 CSARDPSRGSGVMDEQF TRBV2 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 97% sanger CD8+ HIV+ 3963I KK10 PBMC 35 | 34 CSARDPPRGSGVMDEQF TRBV2 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 2% sanger CD8+ HIV+ 3963I KK10 PBMC 36 | 35 CSADPSRGSGVMDEQF TRBV2-1 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 2% sanger CD8+ HIV+ 3963I KK10 PBMC 37 | 36 CASSLDRETGY TRBV6-4 TRBJ2-5 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 78% sanger CD8+ HIV+ 2714A KK10 PBMC 38 | 37 CASSDRTVRAYEQY TRBV6-4 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 7% sanger CD8+ HIV+ 2714A KK10 PBMC 39 | 38 CASSRSWLAGGLSTDTQY TRBV17 TRBJ2-3 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 5% sanger CD8+ HIV+ 2714A KK10 PBMC 40 | 39 CASSHDRDTQY TRBV6-4 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 4% sanger CD8+ HIV+ 2714A KK10 PBMC 41 | 40 CASSPLGTRAYEQY TRBV6-4 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 2% sanger CD8+ HIV+ 2714A KK10 PBMC 42 | 41 CASSPLGPSAYEQY TRBV6-4 TRBJ2-7 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 2% sanger CD8+ HIV+ 2714A KK10 PBMC 43 | 42 CASSPGVFGNEQF TRBV5 TRBJ2-1 HomoSapiens HLA-B*27 B2M MHCI KRWIILGLNK Gag HIV-1 PMID:15753288 tetramer-sort 2% sanger CD8+ HIV+ 2714A KK10 PBMC 44 | -------------------------------------------------------------------------------- /chunks/PMID_15849183.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CALSGFYNTDKLIF TRAV19 TRAJ34 CASSIGTGGSQPQHF TRBV7-2 TRBJ1-5 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 2/10 sanger antigen-loaded-targets SB9 CTL culture 3 | 2 CALSGFYNTDKLIF TRAV19 TRAJ34 CASSKLGTSEETQYF TRBV5-6 TRBJ2-5 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 1/10 sanger antigen-loaded-targets SB32 CTL culture 4 | 3 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 5 | 4 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGETEAFF TRBV6-1 TRBJ1-1 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 1/1 sanger antigen-loaded-targets CA5 CTL culture 6 | 5 CVVSCSGNTGKLIF TRAV10 TRAJ37 CASPGETEAFF TRBV6-1 TRBJ1-1 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 1/1 sanger antigen-loaded-targets CA5 CTL culture 7 | 6 CALRDPTGANSKLTF TRAV16 TRAJ56 CASSRTGSTYEQYF TRBV5-6 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 1/10 sanger antigen-loaded-targets SB47 CTL culture 8 | 7 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI GPEPLPQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 9 | 8 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEGLPQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 10 | 9 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLGQGQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 11 | 10 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQAQLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 12 | 11 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGGLTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 13 | 12 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQGTAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 14 | 13 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQLGAY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 15 | 14 CALSGFYNTDKLIF TRAV19 TRAJ34 CASPGLAGEYEQYF TRBV6-1 TRBJ2-7 HomoSapiens HLA-B*35:08 B2M MHCI LPEPLPQGQLTGY BZLF1 EBV PMID:15849183 antigen-expressing-targets 6/10 sanger antigen-loaded-targets SB27 CTL culture 16 | -------------------------------------------------------------------------------- /chunks/PMID_16326979.txt: -------------------------------------------------------------------------------- 1 | cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id submitter method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id comment 2 | CILPLAGGTSYGKLTF TRAV26-2 TRAJ52 CASSLGQAYEQYF TRBV7-8 TRBJ2-7 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:16326979 Ivan Zvyagin CTL clone 21/21 sanger pentamer-sort healthy donor 1 PBMC 18 years follow-up 3 | CIVWGGYQKVTF TRAV26 TRAJ13 CASRYRDDSYNEQFF TRBV7-9 TRBJ2-1 HomoSapiens HLA-B*44:05 B2M MHCI EENLLDFVRF EBNA3A EBV PMID:16326979 Ivan Zvyagin tetramer-sort 27/27 sanger CTL clone CD8 6.6% of CD8 cells healthy donor 2 PBMC 11 years follow-up 4 | -------------------------------------------------------------------------------- /chunks/PMID_17459926.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSTGSAPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/11 sanger CMV-seropositive D2 HLA-B*35:01 3 | 2 CASSSGTGPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/10 sanger CMV-seropositive D4 HLA-B*35:01 4 | 3 CASSSGTGPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/11 sanger CMV-seropositive D2 HLA-B*35:01 5 | 4 CASSSGTAPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/11 sanger CMV-seropositive D5 HLA-B*35:01 6 | 5 CASTSGTGPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 3/10 sanger CMV-seropositive D4 HLA-B*35:01 7 | 6 CASSPGTGPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/11 sanger CMV-seropositive D5 HLA-B*35:01 8 | 7 CASTPGTGPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 8/9 sanger CMV-seropositive D3 HLA-B*35:01 9 | 8 CASSPPTAPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 3/19 sanger CMV-seropositive D1 HLA-B*35:01 10 | 9 CASSPGTAPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 4/10 sanger CMV-seropositive D4 HLA-B*35:01 11 | 10 CASSLPSGPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/11 sanger CMV-seropositive D2 HLA-B*35:01 12 | 11 CASSLASTPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 3/19 sanger CMV-seropositive D1 HLA-B*35:01 13 | 12 CASSPGTEPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/9 sanger CMV-seropositive D3 HLA-B*35:01 14 | 13 CASSPSSGPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/10 sanger CMV-seropositive D4 HLA-B*35:01 15 | 14 CASSPTTAPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/10 sanger CMV-seropositive D4 HLA-B*35:01 16 | 15 CASSLSTAPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/11 sanger CMV-seropositive D5 HLA-B*35:01 17 | 16 CASTPQTAPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 2/11 sanger CMV-seropositive D2 HLA-B*35:01 18 | 17 CASSPSREPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 7/11 sanger CMV-seropositive D5 HLA-B*35:01 19 | 18 CASSAETGPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 5/11 sanger CMV-seropositive D2 HLA-B*35:01 20 | 19 CASSASDSPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/11 sanger CMV-seropositive D5 HLA-B*35:01 21 | 20 CASSPPANPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 12/19 sanger CMV-seropositive D1 HLA-B*35:01 22 | 21 CATSTGETPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/19 sanger CMV-seropositive D1 HLA-B*35:01 23 | 22 CATETSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 3/11 sanger CMV-seropositive D4 HLA-B*35:01 24 | 23 CATETSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 9/12 sanger CMV-seropositive D2 HLA-B*35:01 25 | 24 CATEDSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 7/11 sanger CMV-seropositive D4 HLA-B*35:01 26 | 25 CATEDSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 5/9 sanger CMV-seropositive D1 HLA-B*35:01 27 | 26 CATEDSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 5/6 sanger CMV-seropositive D3 HLA-B*35:01 28 | 27 CVTEDSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/6 sanger CMV-seropositive D3 HLA-B*35:01 29 | 28 CAREDSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 1/11 sanger CMV-seropositive D4 HLA-B*35:01 30 | 29 CAYEGSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 6/10 sanger CMV-seropositive D5 HLA-B*35:01 31 | 30 CATEGSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 3/12 sanger CMV-seropositive D2 HLA-B*35:01 32 | 31 CATEGSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 3/10 sanger CMV-seropositive D5 HLA-B*35:01 33 | 32 CATEGSNYQLIW TRAV17 TRAJ33 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort 4/9 sanger CMV-seropositive D1 HLA-B*35:01 34 | 33 CATETSNYQLIW TRAV17 TRAJ33 CASSPGTAPNEKLFF TRBV28 TRBJ1-4 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:17459926 tetramer-sort,cultured-T-cells 4/4 sanger CMV-seropositive HLA-B*35:01 35 | -------------------------------------------------------------------------------- /chunks/PMID_17709536.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CATEIRMDSSYKLIFG TRAV12 TRAJ12 CASSSRDRGPHGQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ primary-infection 104 TPR PBMC 3 | 2 CATEGRMDSSYKLIFG TRAV3 TRAJ12 CASSSRDLGEYEQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ primary-infection 104 TPR PBMC 4 | 3 CATRPPGAGSYQLTFG TRAV12 TRAJ28 CASSHDYRGRRSPLHFG TRBV6S4 TRBJ1-6 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ primary-infection 104 TPR PBMC 5 | 4 CATVSRMDSSYKLIFG TRAV3 TRAJ12 CASSLIGEGTGWHQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ primary-infection 104 TPR PBMC 6 | 5 CATEGRMDSSYKLIFG TRAV3 TRAJ12 CASSLVGVGLLLNEQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ primary-infection 104 TPR PBMC 7 | 6 CASSGVGGWDEQYFG TRBV1 TRBJ2-7 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ primary-infection 106 NLV PBMC 8 | 7 CADYYGQNFVFG TRAV16 TRAJ26 CASSFQGYTEAFFG TRBV3 TRBJ1-1 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ primary-infection 106 NLV PBMC 9 | 8 CASNTGNQFYFG TRAV18 TRAJ49 CASSPVTGTGHYGYTFG TRBV13S1 TRBJ1-2 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ primary-infection 106 NLV PBMC 10 | 9 CAWVPTGTGGTEAFFG TRBV20 TRBJ1-1 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ primary-infection 106 NLV PBMC 11 | 10 CASSSHDRQGASSPLHFG TRBV6S4 TRBJ1-6 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier H0018 TPR PBMC 12 | 11 CASSSHDREGGSSPLHFG TRBV6S4 TRBJ1-6 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier H0018 TPR PBMC 13 | 12 CASSSHDTGGYNSPLHFG TRBV6S4 TRBJ1-6 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier 002 TPR PBMC 14 | 13 CASSTHDIQGLGSPLHFG TRBV6S4 TRBJ1-6 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier 025 TPR PBMC 15 | 14 CASSSHDYRGRRSPLHFG TRBV6S4 TRBJ1-6 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ carrier 104 TPR PBMC 16 | 15 CASSFRDYGNYEQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier 002 TPR PBMC 17 | 16 CASSNRDRGDYEQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ carrier 018 TPR PBMC 18 | 17 CASSSRDRGPHGQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ carrier 104 TPR PBMC 19 | 18 CASSSRDLGEYEQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ carrier 104 TPR PBMC 20 | 19 CASSLRDRGSYEQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier 3574666 TPR PBMC 21 | 20 CASSSRDRGSYEQYFG TRBV6S4 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier 6017009 TPR PBMC 22 | 21 CASSPTTGTGHYGYTFG TRBV13S1 TRBJ1-2 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier 008 NLV PBMC 23 | 22 CASSYQTGTGVYGYTFG TRBV13S1 TRBJ1-2 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier 004 NLV PBMC 24 | 23 CASSYQTGTGNYGYTFG TRBV13S1 TRBJ1-2 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger CD8+ carrier 001 NLV PBMC 25 | 24 CASSPVTGTGHYGYTFG TRBV13S1 TRBJ1-2 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:17709536 tetramer-sort,limiting-dilution-cloning sanger antigen-loaded-targets CD8+ carrier 106 NLV PBMC 26 | -------------------------------------------------------------------------------- /chunks/PMID_18270323.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAVSDKNRDDKIIF TRAV8-6*02 TRAJ30*01 CASRPGTASYEQYF TRBV28*01 TRBD1*01 TRBJ2-7*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 4/4 sanger CD8+ healthy 1 10 clone 3 | 2 CASRPGTASYEQYF TRBV28*01 TRBD1*01 TRBJ2-7*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 2/7 sanger CD8+ healthy 1 Polyclonal T-cell line 4 | 3 CAVSDKNRDDKIIF TRAV8-6*02 TRAJ30*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 1/7 sanger CD8+ healthy 1 Polyclonal T-cell line 5 | 4 CAVSAPYNTDKLIFF TRAV8-6*02 TRAJ34*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 3/7 sanger CD8+ healthy 1 Polyclonal T-cell line 6 | 5 CAVRPSGGSYIPTF TRAV8-6*02 TRAJ6*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 1/7 sanger CD8+ healthy 1 Polyclonal T-cell line 7 | 6 CASRPGTSSYEQYF TRBV28*01 TRBD1*01 TRBJ2-7*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 8/22 sanger CD8+ healthy 6 Polyclonal T-cell line 8 | 7 CAVSDKNRDDKIIF TRAV8-6*02 TRAJ30*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 10/22 sanger CD8+ healthy 6 Polyclonal T-cell line 9 | 8 CAVSANYGGSQGNLIF TRAV8-6*02 TRAJ42*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 4/22 sanger CD8+ healthy 6 Polyclonal T-cell line 10 | 9 CASRPGTSSYEQYF TRBV28*01 TRBD2*01 TRBJ2-7*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 6/11 sanger CD8+ healthy 2 Polyclonal T-cell line 11 | 10 CAVSDKNRDDKIIF TRAV8-6*02 TRAJ30*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 5/11 sanger CD8+ healthy 2 Polyclonal T-cell line 12 | 11 CASRPGTSSYEQYF TRBV28*01 TRBD2*01 TRBJ2-7*01 HomoSapiens HLA-B*35:08 B2M MHCI CPSQEPMSIYVY pp65 CMV PMID:18270323 pentamer-sort 7/7 sanger CD8+ healthy 2 PBMC 13 | 12 CAWSEPQNLPSLYGYTF TRBV30*01 TRBJ1-2*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 11/13 sanger CD8+ healthy 1 PBMC 14 | 13 CAWSVASGANNEQFF TRBV30*01 TRBD2*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 1/13 sanger CD8+ healthy 1 PBMC 15 | 14 CAWSVAAGILEQFF TRBV30*01 TRBD2*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 1/13 sanger CD8+ healthy 1 PBMC 16 | 15 CASSLVAGYGSYNEQFF TRBV7-6*01 TRBD1*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 3/3 sanger CD8+ healthy 2 15 clone 17 | 16 CASSLVAGYGSYNEQFF TRBV7-6*01 TRBD1*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 3/3 sanger CD8+ healthy 2 4 clone 18 | 17 CASSLVAGYGSYNEQFF TRBV7-6*01 TRBD1*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 4/4 sanger CD8+ healthy 2 7 clone 19 | 18 CASSLVAGYGSYNEQFF TRBV7-6*01 TRBD1*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 4/4 sanger CD8+ healthy 2 10 clone 20 | 19 CASSLVAGYGSYNEQFF TRBV7-6*01 TRBD1*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 5/5 sanger CD8+ healthy 2 Polyclonal T-cell line 21 | 20 CASSQDRASPLHEQFF TRBV4-3*01 TRBD2*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 8/10 sanger CD8+ healthy 6 Polyclonal T-cell line 22 | 21 CASSQDWGDGYTF TRBV4-2*01 TRBD2*01 TRBJ1-2*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 1/10 sanger CD8+ healthy 6 Polyclonal T-cell line 23 | 22 CASSQVGHEQFF TRBV4-3*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 1/10 sanger CD8+ healthy 6 Polyclonal T-cell line 24 | 23 CAWSPTGDQPQHF TRBV30*05 TRBD1*01 TRBJ1-5*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 2/5 sanger CD8+ healthy 1 Polyclonal T-cell line 25 | 24 CAWSEPGLDQPQHF TRBV30*05 TRBD1*01 TRBJ1-5*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 1/5 sanger CD8+ healthy 1 Polyclonal T-cell line 26 | 25 CAWSVAAGILEQFF TRBV30*05 TRBD2*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 1/5 sanger CD8+ healthy 1 Polyclonal T-cell line 27 | 26 CAWSLASGGTDNEQFF TRBV30*05 TRBD2*01 TRBJ2-1*01 HomoSapiens HLA-B*35:08 B2M MHCI FPTKDVAL pp65 CMV PMID:18270323 pentamer-sort 1/5 sanger CD8+ healthy 1 Polyclonal T-cell line 28 | -------------------------------------------------------------------------------- /chunks/PMID_19776383.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASAGETQYF TRBV11-3 TRBJ2-5 HomoSapiens HLA-A*02:01 B2M MHCI EDVPSGKLFMHVTLG pp65 CMV PMID:19776383 antigen-loaded-targets sanger CD8+ post-transplant PBMC 3 | 2 CASTDGQKNSPLHF TRBV6-5 TRBJ1-6 HomoSapiens HLA-A*02:01 B2M MHCI ARNLVPMVATVQGQN pp65 CMV PMID:19776383 antigen-loaded-targets sanger CD8+ post-transplant PBMC 4 | 3 CASSYNSAGYNEQF TRBV6-6 TRBJ2-1 HomoSapiens HLA-A*02:01 B2M MHCI ARNLVPMVATVQGQN pp65 CMV PMID:19776383 antigen-loaded-targets sanger CD8+ post-transplant PBMC 5 | 4 CATESTGIGGYTFTW TRBV25-1 TRBJ1-2 HomoSapiens HLA-A*02:01 B2M MHCI ARNLVPMVATVQGQN pp65 CMV PMID:19776383 antigen-loaded-targets sanger CD8+ post-transplant PBMC 6 | 5 CASSFATGTAYGYTF TRBV6-5 TRBJ1-2 HomoSapiens HLA-A*02:01 B2M MHCI LSEFCRVLCCYVLEE IE1 CMV PMID:19776383 antigen-loaded-targets sanger CD8+ post-transplant PBMC 7 | 6 CASSNPQGAKYEQF TRBV6-2 TRBJ2-1 HomoSapiens HLA-A*02:01 B2M MHCI LSEFCRVLCCYVLEE IE1 CMV PMID:19776383 antigen-loaded-targets sanger CD8+ post-transplant PBMC 8 | -------------------------------------------------------------------------------- /chunks/PMID_19864595.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAGPMKTSYDKVIFG TRAV35*02 TRAJ50*01 CASSSANYGYTFG TRBV12-4*01 TRBJ1-2*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:19864595 antigen-loaded-targets sanger multimer-sort,antigen-loaded-targets CD8+ CMV+,EBV+ 6 JG-9/JG-24 TCL culture HLA-A*02:01;HLA-B*35:03,HLA-B*57:01;HLA-C*04,HLA-C*06 3 | 2 CAVFF TRAV3*01 TRAJ35*01 CASSPTGGSPSPLHFG TRBV27*01 TRBJ1-6*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:19864595 antigen-loaded-targets sanger multimer-sort,antigen-loaded-targets CD8+ CMV+,EBV+ 6 JG-33 TCL culture HLA-A*02:01;HLA-B*35:03,HLA-B*57:01;HLA-C*04,HLA-C*06 4 | 3 CVAWGGYSSASKIIFG TRAV12-1*01 TRAJ3*01 CASSVVGDEQYFG TRBV9*01 TRBJ2-7*01 HomoSapiens HLA-A*01:01 B2M MHCI YSEHPTFTSQY pp65 CMV PMID:19864595 antigen-expressing-targets sanger multimer-sort,antigen-loaded-targets CD8+ CMV+,EBV+ 7 MD-19 TCL culture HLA-A*01,HLA-A*11;HLA-B*08,HLA-B*15:01;HLA-C*03,HLA-C*07 5 | 4 CAERGWDNDMRFG TRAV5*01 TRAJ43*01 CASSADSNGELFFG TRBV11-2*01 TRBJ2-2*01 HomoSapiens HLA-B*35:01 B2M MHCI IPSINVHHY pp65 CMV PMID:19864595 antigen-loaded-targets sanger multimer-sort,antigen-loaded-targets CD8+ CMV+,EBV+ 8 BF-33/BF-38 TCL culture HLA-A*02,HLA-A*03;HLA-B*35,HLA-B*40:01;HLA-C*03,HLA-C*15 6 | -------------------------------------------------------------------------------- /chunks/PMID_20432235.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSEEGAWNTGELF TRBV6-1 TRBJ2-2 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 90% sanger CD8+ healthy p7 TV9 A02:01,A11,B18,B27 3 | 2 CASSHTSGGLKDTQY TRBV3-1 TRBJ2-3 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 10% sanger CD8+ healthy 7 TV9 A02:01,A11,B18,B27 4 | 3 CASSPRGDWEEKAGELF TRBV4-3 TRBJ2-2 HomoSapiens HLA-A*02:01 B2M MHCI KINAWIKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 77% sanger CD8+ healthy 7 TV9p6 A02:01,A11,B18,B27 5 | 4 CASSEEGAWNTGELF TRBV6-1 TRBJ2-2 HomoSapiens HLA-A*02:01 B2M MHCI KINAWIKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 15% sanger CD8+ healthy 7 TV9p6 A02:01,A11,B18,B27 6 | 5 CSVEDPDRGYEQY TRBV29-1 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI KINAWIKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 8% sanger CD8+ healthy 7 TV9p6 A02:01,A11,B18,B27 7 | 6 CASSRRGDGFQPQH TRBV27 TRBJ1-3 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 36% sanger CD8+ healthy 6 TV9 A02:01,A29,B40,B44 8 | 7 CASRDFYNEQF TRBV6-6 TRBJ2-1 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 29% sanger CD8+ healthy 6 TV9 A02:01,A29,B40,B44 9 | 8 CSAFSSGTGGVTGELF TRBV20-1 TRBJ2-2 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 14% sanger CD8+ healthy 6 TV9 A02:01,A29,B40,B44 10 | 9 CASSQDPSPSTDTQY TRBV4-3 TRBJ2-3 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 7% sanger CD8+ healthy 6 TV9 A02:01,A29,B40,B44 11 | 10 CASSLWGLAPDNEQF TRBV7-8 TRBJ2-1 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 7% sanger CD8+ healthy 6 TV9 A02:01,A29,B40,B44 12 | 11 CASSLWGGPMETQY TRBV27 TRBJ2-5 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 7% sanger CD8+ healthy 6 TV9 A02:01,A29,B40,B44 13 | 12 CSAFSSGTGGVTGELF TRBV20-1 TRBJ2-2 HomoSapiens HLA-A*02:01 B2M MHCI KINAWIKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 82% sanger CD8+ healthy 6 TV9p6 A02:01,A29,B40,B44 14 | 13 CASSLVPQGEEQY TRBV7-2 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI KINAWIKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 6% sanger CD8+ healthy 6 TV9p6 A02:01,A29,B40,B44 15 | 14 CSAFSSGTGGVTGEPF TRBV20-1 TRBJ2-2 HomoSapiens HLA-A*02:01 B2M MHCI KINAWIKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 6% sanger CD8+ healthy 6 TV9p6 A02:01,A29,B40,B44 16 | 15 CSAFSSGTEGVTGELF TRBV20-1 TRBJ2-2 HomoSapiens HLA-A*02:01 B2M MHCI KINAWIKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 6% sanger CD8+ healthy 6 TV9p6 A02:01,A29,B40,B44 17 | 16 CASSLVPQGEEQY TRBV7-2 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 88% sanger CD8+ healthy 9 TV9 A02:01,A24,B15,B40 18 | 17 CASSLVPQGEEPY TRBV7-2 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 12% sanger CD8+ healthy 9 TV9 A02:01,A24,B15,B40 19 | 18 CASSYRGQSYEQY TRBV28-0 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 94% sanger CD8+ healthy 3 TV9 A02:01 20 | 19 CSGRDSYTEAF TRBV29-1 TRBJ1-1 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 4% sanger CD8+ healthy 3 TV9 A02:01 21 | 20 CASSEYRGPSSYEQY TRBV5-8 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 1% sanger CD8+ healthy 3 TV9 A02:01 22 | 21 CASSCRGQSYEQY TRBV28-0 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 1% sanger CD8+ healthy 3 TV9 A02:01 23 | 22 CSARDAGGDYGYT TRBV20-1 TRBJ1-2 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 69% sanger CD8+ healthy 2 TV9 A02:01,B15,B40 24 | 23 CASSDTGELF TRBV12-4 TRBJ2-2 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 26% sanger CD8+ healthy 2 TV9 A02:01,B15,B40 25 | 24 CASSQVKIGQGNEKLF TRBV3-1 TRBJ1-4 HomoSapiens HLA-A*02:01 B2M MHCI TLNAWVKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 6% sanger CD8+ healthy 2 TV9 A02:01,B15,B40 26 | 25 CSASRDSYEQY TRBV20-1 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI KINAWIKVV Gag HIV-1 PMID:20432235 cultured-T-cells,tetramer-sort 100% sanger CD8+ healthy 2 TV9p6 A02:01,B15,B40 27 | -------------------------------------------------------------------------------- /chunks/PMID_22044339.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASNPGTGTDTQYF TRBV10-1*01 TRBJ2-3*01 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 5/9 sanger AML,HSCT 4 3 | 2 CASNPGTGADEQYF TRBV10-1*01 TRBJ2-7*01 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 2/9 sanger AML,HSCT 4 4 | 3 CASNAGTGNEQYF TRBV10-1*01 TRBJ2-7*01 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 1/9 sanger AML,HSCT 4 5 | 4 CASNAGTGTDTQYF TRBV10-1*01 TRBJ2-3*01 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 1/9 sanger AML,HSCT 4 6 | 5 CAISVAARGEQFF TRBV10-3*01 TRBJ2-1*01 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 4/9 sanger MM,HSCT 9 7 | 6 CAISETTRGDSPLHF TRBV10-3*01 TRBJ1-6*01 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 2/9 sanger MM,HSCT 9 8 | 7 CAISGRGDTEAFF TRBV10-3*01 TRBJ1-1*01 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 8/8 sanger AML,HSCT 8 9 | 8 CASSLGAGTFKTNEKLFF TRBV7-4 TRBJ1-4 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 9/11 sanger AML,HSCT 8 10 | 9 CASSLTDGDQPQHF TRBV7-3 TRBJ1-5 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 1/11 sanger AML,HSCT 8 11 | 10 CASSLVASQETQYF TRBV7-4 TRBJ2-5 HomoSapiens HLA-B*35 B2M MHCI IPSINVHHY pp65 CMV PMID:22044339 tetramer-sort 1/10 sanger MM,HSCT 9 12 | -------------------------------------------------------------------------------- /chunks/PMID_22314361.txt: -------------------------------------------------------------------------------- 1 | cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id submitter method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id comment 2 | CASSYSGGVGETQY TRBV6-5 TRBJ2-5 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 3 | CASSYSGGVGETQY TRBV6-5 TRBJ2-5 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLRT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 4 | CASSDGTFTEAF TRBV25-1 TRBJ1-1 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 5 | CASSMSPGPRESPLH TRBV9 TRBJ1-6 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 6 | CASSMSPGPRESPLH TRBV9 TRBJ1-6 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLRT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 7 | CASSDAGLGDYEQY TRBV25-1 TRBJ2-7 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 8 | CASSDAGLGDYEQY TRBV25-1 TRBJ2-7 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLRT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 9 | CASSPPGAGEGETQY TRBV28 TRBJ2-5 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 10 | CASSPPGAGEGETQY TRBV28 TRBJ2-5 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLRT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 11 | CASSLIAEEEGYGYT TRBV28 TRBJ1-2 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 12 | CASSTTGSTDTQY TRBV28 TRBJ2-3 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 13 | CASSLGLAGGGDTQY TRBV5-4 TRBJ2-3 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 14 | CASTPGTGDVQPQH TRBV28 TRBJ1-5 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 15 | CASSPLSQGVRGYT TRBV5-6 TRBJ1-2 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 16 | CASSPLSQGVRGYT TRBV5-6 TRBJ1-2 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAR HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 17 | CASSRTGSTDTQY TRBV28 TRBJ2-3 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 18 | CASSTDRGPYEQY TRBV4-1 TRBJ2-7 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 19 | CATSDESYGYT TRBV24-1 TRBJ1-2 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 20 | CASSRLRGPYEQY TRBV28 TRBJ2-7 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 21 | CASSYDPSPTYEQY TRBV6-5 TRBJ2-7 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 22 | CASSDAGLGDYEQY TRBV25-1 TRBJ2-3 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 23 | CAYTTSGAVTDTQY TRBV30 TRBJ2-3 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 24 | CASSEGFGAFQPQH TRBV12-3,TRBV12-4 TRBJ1-5 HomoSapiens HLA-DRA*01 HLA-DRB1*01 MHCII PKYVKQNTLKLAT HA InfluenzaA PMID:22314361 Anastasiia Sycheva tetramer-sort,antigen-loaded-targed sanger CD4+ healthy HA305-320 PBMC HLA-DR1 25 | -------------------------------------------------------------------------------- /chunks/PMID_22323539.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSPHRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 10/10 rna-seq CD8+ 1 55170 PBMC 3 | 2 CASSPNRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 9/10 rna-seq CD8+ 3 55170 PBMC 4 | 3 CASSPSRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/10 rna-seq CD8+ 3 55170 PBMC 5 | 4 CASSPARNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 5/10 rna-seq CD8+ 4 55170 PBMC 6 | 5 CASSPSRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 5/10 rna-seq CD8+ 4 55170 PBMC 7 | 6 CASSPHRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 7/11 rna-seq CD8+ 6 55170 PBMC 8 | 7 CASSPQRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 4/11 rna-seq CD8+ 6 55170 PBMC 9 | 8 CASSPSRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 5/9 rna-seq CD8+ 7 55170 PBMC 10 | 9 CASSPYRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 3/9 rna-seq CD8+ 7 55170 PBMC 11 | 10 CASSPHRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/9 rna-seq CD8+ 7 55170 PBMC 12 | 11 CASSPARNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 2/8 rna-seq CD8+ 8 55170 PBMC 13 | 12 CASSPQRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/8 rna-seq CD8+ 8 55170 PBMC 14 | 13 CASSPTRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 2/8 rna-seq CD8+ 8 55170 PBMC 15 | 14 CASSPSRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 3/8 rna-seq CD8+ 8 55170 PBMC 16 | 15 CASSPSRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 8/8 rna-seq CD8+ 9 55170 PBMC 17 | 16 CASSPQRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 11/15 rna-seq CD8+ 10 55170 PBMC 18 | 17 CASSPQRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/13 rna-seq CD8+ 10 55170 PBMC 19 | 18 CASSPSRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 3/15 rna-seq CD8+ 10 55170 PBMC 20 | 19 CASSPQRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 9/9 rna-seq CD8+ 11 55170 PBMC 21 | 20 CASSPARNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/9 rna-seq CD8+ 14 55170 PBMC 22 | 21 CASSPTRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/9 rna-seq CD8+ 14 55170 PBMC 23 | 22 CASSPSRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 7/9 rna-seq CD8+ 14 55170 PBMC 24 | 23 CASSKGAAITVGLETQYF TRBV2 TRBJ2-5 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 8/8 rna-seq CD8+ 19 55170 PBMC 25 | 24 CSARDLKAGSWVEQYF TRBV20-1 TRBJ2-7 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 11/11 rna-seq CD8+ 19 55170 PBMC 26 | 25 CASSQGLAGGPRTDTQYF TRBV4-1 TRBJ2-3 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 9/9 rna-seq CD8+ 19 55170 PBMC 27 | 26 CAISEGDLNTEAFF TRBV10-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 9/9 rna-seq CD8+ 19 55170 PBMC 28 | 27 CASSPQSDQNQGTQYF TRBV5-1 TRBJ2-5 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 10/16 rna-seq CD8+ 21 55170 PBMC 29 | 28 CASSGDPEHGYNYGYTF TRBV5-1 TRBJ1-2 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 5/16 rna-seq CD8+ 21 55170 PBMC 30 | 29 CASSLASDGPQETQYF TRBV5-1 TRBJ2-5 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/16 rna-seq CD8+ 21 55170 PBMC 31 | 30 CSGIDKPVTDTQYF TRBV29-1 TRBJ2-3 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 7/7 rna-seq CD8+ 22 55170 PBMC 32 | 31 CSASLASTSNYGYTF TRBV20-1 TRBJ1-2 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 10/10 rna-seq CD8+ 22 55170 PBMC 33 | 32 CASSEGIGYNSPLHF TRBV27 TRBJ1-6 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 20/20 rna-seq CD8+ 22 55170 PBMC 34 | 33 CASSWAPNTGELF TRBV12-3 TRBJ2-2 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 10/10 rna-seq CD8+ 23 55170 PBMC 35 | 34 CSATPARASNTEAFF TRBV20-1 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 14/16 rna-seq CD8+ 23 55170 PBMC 36 | 35 CSARDPQGVTEAFF TRBV20-1 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/16 rna-seq CD8+ 23 55170 PBMC 37 | 36 CSARDSSGGAKNIQYF TRBV20-1 TRBJ2-4 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 1/16 rna-seq CD8+ 23 55170 PBMC 38 | 37 CAASIGDFGNEKLTF TRAV23 TRAJ48 CASSPYRNTEAFF TRBV4-3 TRBJ1-1 HomoSapiens HLA-B*07:02 B2M MHCI RPHERNGFTVL pp65 CMV PMID:22323539 antigen-loaded-targets,pentamer-sort 3/3 rna-seq CD8+ 7 55170 PBMC 39 | -------------------------------------------------------------------------------- /chunks/PMID_23637823.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSGEGAKTTNTEAFF TRBV2*01 TRBD1*01 TRBJ1-1*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort 38/100 yes sanger multimer-sort CD8+ 3 3G PBMC 3 | 2 CASSSTQGKVYEQYF TRBV27*01 TRBD1*01 TRBJ2-7*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort yes sanger CD8+ 3 3H PBMC 4 | 3 CAYRSARDSSYKLIF TRAV38-2/DV8*01 TRAJ12*01 CASSDHSVTGISSPLHF TRBV7-9*03 TRBD1*01 TRBJ1-6*02 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:23637823 multimer-sort 11/12 yes sanger CD8+ 1 1A PBMC 5 | 4 CATVLRMDSSYKLIF TRAV17*01 TRAJ12*01 CASSLIGVSSYNEQFF TRBV7-9*03 TRBD2*01 TRBJ2-1*01 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:23637823 multimer-sort 1/12 yes sanger CD8+ 1 1B PBMC 6 | 5 CAENMGYGNKLVF TRAV13-2*01 TRAJ47*01 CASSYSGQGSAAGETQYF TRBV6-6*01 TRBD1*01 TRBJ2-5*01 HomoSapiens HLA-B*08 B2M MHCI ELRRKMMYM IE1 CMV PMID:23637823 multimer-sort 24/25 yes sanger multimer-sort CD8+ 2 2A PBMC 7 | 6 CAVNKGYGQNFVF TRAV12-2*02 TRAJ26*01 CASSPAGISYNSPLHF TRBV7-9*03 TRBD1*01 TRBJ1-6*01 HomoSapiens HLA-B*08 B2M MHCI ELRRKMMYM IE1 CMV PMID:23637823 multimer-sort 1/25 yes sanger CD8+ 2 2B PBMC 8 | 7 CAVRDSSYSGAGSYQLTF TRAV3*01 TRAJ28*01 CASSRLAGASTDTQYF TRBV7-3*01 TRBD2*01 TRBJ2-3*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort yes sanger CD8+ 3 3A PBMC 9 | 8 CAVSDYGQNFVF TRAV21*01 TRAJ26*01 CASSRLSSNTDTQYF TRBV7-3*01 TRBJ2-3*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort yes sanger CD8+ 3 3B PBMC 10 | 9 CATAQVYSGGGADGLTF TRAV17*01 TRAJ45*01 CASSRLAGNTDTQYF TRBV7-3*01 TRBD2*01 TRBJ2-3*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort yes sanger CD8+ 3 3C PBMC 11 | 10 CVGNSYGQNFVF TRAV12-1*01 TRAJ26*01 CASSRLAGGTDTQYF TRBV7-3*01 TRBD2*02 TRBJ2-3*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort yes sanger multimer-sort CD8+ 3 3D PBMC 12 | 11 CAVNDYGQNFVF TRAV1-1*01 TRAJ26*01 CASSRLAASTDTQYF TRBV7-3*01 TRBD2*01 TRBJ2-3*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort yes sanger multimer-sort CD8+ 3 3E PBMC 13 | 12 CAFMTLRGNTGTASKLTF TRAV38-1*01 TRAJ44*01 CASSLRVNTEAFF TRBV7-3*01 TRBD1*01 TRBJ1-1*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort yes sanger CD8+ 3 3F PBMC 14 | 13 CAASSYGQNFVF TRAV23/DV6*01 TRAJ26*01 CASSRLAANTDTQYF TRBV7-3*01 TRBD2*01 TRBJ2-3*01 HomoSapiens HLA-B*08 B2M MHCI QIKVRVDMV IE1 CMV PMID:23637823 multimer-sort yes sanger CD8+ 3 3I PBMC 15 | 14 CAMREVLYNTDKLIF TRAV14/DV4*01 TRAJ34*01 CASSDLDSGVNTEAFF TRBV2*01 TRBD1*01 TRBJ1-1*01 HomoSapiens HLA-A*02 B2M MHCI RMFPNAPYL WT1 HomoSapiens http://mediatum.ub.tum.de/doc/1136748 multimer-sort yes sanger CD8+ pool allo-alpha18 PBMC 16 | 15 CAASLYDKVIF TRAV29/DV5*01 TRAJ50*01 CATAQGLSSYEQYF TRBV12-4*01 TRBD2*01 TRBJ2-7*01 HomoSapiens HLA-A*02 B2M MHCI RMFPNAPYL WT1 HomoSapiens http://mediatum.ub.tum.de/doc/1136748 multimer-sort yes sanger CD8+ pool allo-alpha40 PBMC 17 | 16 CAYWDSGYALNF TRAV38-2/DV8*01 TRAJ41*01 CACPGPLTYEQYF TRBV30*01 TRBD1*01 TRBJ2-7*01 HomoSapiens HLA-A*02 B2M MHCI RMFPNAPYL WT1 HomoSapiens http://mediatum.ub.tum.de/doc/1136748 multimer-sort yes sanger CD8+ pool allo-alpha46 PBMC 18 | 17 CAVNDQGGGADGLTF TRAV12-2*02 TRAJ45*01 CASSWWDTGELFF TRBV6-2*01 TRBD1*01 TRBJ2-2*01 HomoSapiens HLA-A*02 B2M MHCI RMFPNAPYL WT1 HomoSapiens PMID:23637823 multimer-sort 3/4 yes sanger multimer-sort,antigen-loaded-targets CD8+ pool TCR5B PBMC 19 | 18 CAVSEGGDYKLSF TRAV8-4*03 TRAJ20*01 CAWGTLATEQYF TRBV28*01 TRBD2*01 TRBJ2-7*01 HomoSapiens HLA-A*02 B2M MHCI RMFPNAPYL WT1 HomoSapiens PMID:23637823 multimer-sort 1/4 yes sanger multimer-sort,antigen-loaded-targets CD8+ pool TCR5A PBMC 20 | 19 CAMSLYYGGSQGNLIF TRAV14 TRAJ42*01 CASSLEIFGGIADTDTQYF TRBV11-2*01 TRBD2*01 TRBJ2-3*01 HomoSapiens HLA-A*02 B2M MHCI KIFGSLAFL ERBB2 HomoSapiens PMID:23637823 multimer-sort yes sanger multimer-sort,antigen-loaded-targets CD8+ pool 4A PBMC 21 | -------------------------------------------------------------------------------- /chunks/PMID_23933763.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSDPGDSLNGYTF TRBV5 TRBJ1-1 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 231/330 CMV-seropositive Case-1 N-1 HLA-A*24:02 3 | 2 CASSSTGGGGTEAFF TRBV7 TRBJ1-1 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 66/330 CMV-seropositive Case-1 N-2 HLA-A*24:02 4 | 3 CAISDPGHRFGEAFF TRBV10 TRBJ1-1 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 6/330 CMV-seropositive Case-1 N-9 HLA-A*24:02 5 | 4 CSARFSGQGTEAFF TRBV20 TRBJ1-1 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 128/335 CMV-seropositive Case-2 S-1 HLA-A*24:02 6 | 5 CASSSNQGATQYF TRBV7 TRBJ2-3 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 50/335 CMV-seropositive Case-2 S-2 HLA-A*24:02 7 | 6 CASINRGTDPYEQYF TRBV13 TRBJ2-7 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 7/335 CMV-seropositive Case-2 S-3 HLA-A*24:02 8 | 7 CASTPRDRSNYEQYF TRBV27 TRBJ2-7 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 42/335 CMV-seropositive Case-2 S-4 HLA-A*24:02 9 | 8 CASSFTLSPETQYF TRBV7 TRBJ2-5 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 9/335 CMV-seropositive Case-2 S-7 HLA-A*24:02 10 | 9 CASSQGQGAQNQPQHF TRBV4 TRBJ1-5 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 3/335 CMV-seropositive Case-2 S-24 HLA-A*24:02 11 | 10 CAGTGIRSAGELFF TRBV30 TRBJ2-2 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 18/335 CMV-seropositive Case-2 S-32 HLA-A*24:02 12 | 11 CASKPRDSGDTQYF TRBV28 TRBJ2-3 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 4/335 CMV-seropositive Case-2 S-56 HLA-A*24:02 13 | 12 CSARNPGLYEQYF TRBV20 TRBJ2-7 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 3/335 CMV-seropositive Case-2 S-57 HLA-A*24:02 14 | 13 CASSSIQGAAGELFF TRBV7 TRBJ2-2 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 18/268 CMV-seropositive Case-3 I-1 HLA-A*24:02 15 | 14 CASSQVSTGETQYF TRBV14 TRBJ2-5 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 24/268 CMV-seropositive Case-3 I-2 HLA-A*24:02 16 | 15 CASRGQVSSQETQYF TRBV2 TRBJ2-5 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 20/268 CMV-seropositive Case-3 I-3 HLA-A*24:02 17 | 16 CAIKGTVSTQETQYF TRBV2 TRBJ2-5 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 3/268 CMV-seropositive Case-3 I-4 HLA-A*24:02 18 | 17 CASSSTGGGGAEAFF TRBV7 TRBJ1-1 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 50/268 CMV-seropositive Case-3 I-24 HLA-A*24:02 19 | 18 CASDRGGNTGELFF TRBV6 TRBJ2-2 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 25/268 CMV-seropositive Case-3 I-25 HLA-A*24:02 20 | 19 CASSLDTDTQYF TRBV5 TRBJ2-3 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 8/268 CMV-seropositive Case-3 I-26 HLA-A*24:02 21 | 20 CASSPDRGRGYTF TRBV28 TRBJ1-2 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 10/268 CMV-seropositive Case-3 I-27 HLA-A*24:02 22 | 21 CASSLSSTRTDTQYF TRBV7 TRBJ2-3 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 7/268 CMV-seropositive Case-3 I-28 HLA-A*24:02 23 | 22 CASSLNSVGTEAFF TRBV28 TRBJ1-1 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 7/268 CMV-seropositive Case-3 I-29 HLA-A*24:02 24 | 23 CASSSDNAIGGGSYGYTF TRBV28 TRBJ1-2 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 3/268 CMV-seropositive Case-3 I-30 HLA-A*24:02 25 | 24 CASSLGAGGPSDTQYF TRBV5 TRBJ2-3 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 8/268 CMV-seropositive Case-3 I-32 HLA-A*24:02 26 | 25 CASSLGGLAPSTDTQYF TRBV7 TRBJ2-3 HomoSapiens HLA-A*24:02 B2M MHCI QYDPVAALF pp65 CMV PMID:23933763 tetramer-sort 3/268 CMV-seropositive Case-3 I-34 HLA-A*24:02 27 | -------------------------------------------------------------------------------- /chunks/PMID_24069285.txt: -------------------------------------------------------------------------------- 1 | cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id submitter method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id comment 2 | CASSEALLGRANYGYTF TRBV2 TRBJ1-2*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva pentamer-sort 0.0095 amplicon-seq antigen-loaded-targets CD8+ 4 pp65(495) PBMC Full sequence: DSAMYFCASSEALLGRANYGYTFGSGTRLTV, V-segment restored via IgBLAST, see the article for details 3 | CASSLAPGTTNEKLFF TRBV7-6,TRBV7-7 TRBJ1-4*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva pentamer-sort 0.0033 amplicon-seq antigen-loaded-targets CD8+ 5 pp65(495) PBMC Full sequence: RDSAMYRCASSLAPGTTNEKLFFGSGTQLSV, V-segment restored via IgBLAST, see the article for details 4 | CASSPLTGTGVYGYTF TRBV6-6 TRBJ1-2*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva pentamer-sort 0.495 amplicon-seq antigen-loaded-targets CD8+ 7 pp65(495) PBMC Full sequence: SQTSVYFCASSPLTGTGVYGYTFGSGTRLTV, V-segment restored via IgBLAST, see the article for details 5 | CASSSSFPGGGNEQFF TRBV7-2,TRBV7-8,TRBV11-2 TRBJ2-1*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva pentamer-sort 0.0057 amplicon-seq antigen-loaded-targets CD8+ 9 pp65(495) PBMC Full sequence: EDSAVYLCASSSSFPGGGNEQFFGPGTRLTV, V-segment restored via IgBLAST, see the article for details 6 | CASSYATGASYGYTF TRBV6-3,TRBV6-5,TRBV6-9 TRBJ1-2*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva pentamer-sort 0.0172 amplicon-seq antigen-loaded-targets CD8+ 10 pp65(495) PBMC Full sequence: PSQTSVYFCASSYATGASYGYTFGSGTRLTV, V-segment restored via IgBLAST, see the article for details 7 | CASSYQTGAAYGYTF TRBV6-3,TRBV6-5,TRBV6-9 TRBJ1-2*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva pentamer-sort 0.009 amplicon-seq antigen-loaded-targets CD8+ 11 pp65(495) PBMC Full sequence: PSQTSVYFCASSYQTGAAYGYTFGSGTRLTV, V-segment restored via IgBLAST, see the article for details 8 | CASSYQTGASYGYTF TRBV6-3,TRBV6-5,TRBV6-9 TRBJ1-2*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva pentamer-sort 0.247 amplicon-seq antigen-loaded-targets CD8+ 12 pp65(495) PBMC Full sequence: PSQTSVYFCASSYQTGASYGYTFGSGTRLTV, V-segment restored via IgBLAST, see the article for details 9 | CASTLLGGAGYNEQFF TRBV13,TRBV9 TRBJ2-1*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva antigen-loaded-targets amplicon-seq antigen-loaded-targets CD8+ 13 pp65(495) PBMC Full sequence: GDSALYFCASTLLGGAGYNEQFFGPGTRLTV, V-segment restored via IgBLAST, see the article for details 10 | CQQLLFSGGGNEQFF TRBV5-8 TRBJ2-1*01 HomoSapiens HLA-A*02:01 B2M MHCI NLVPMVATV pp65 CMV PMID:24069285 Anastasiia Sycheva pentamer-sort 0.0046 amplicon-seq antigen-loaded-targets CD8+ 14 pp65(495) PBMC Full sequence: GGLRRVSLCQQLLFSGGGNEQFFGPGTRLTV, V-segment restored via IgBLAST, see the article for details 11 | -------------------------------------------------------------------------------- /chunks/PMID_24600035.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSLTGGGELFF TRBV7-3 TRBD2 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 21/21 sanger CD8+ Japanese,HIV-1+ KI-021 TI8 PBMC HLA-B*51:01 3 | 2 CASSLTGGGELFF TRBV7-3 TRBD2 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 13/22 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 4 | 3 CASSSTGGNTIYF TRBV7-3 TRBD1 TRBJ1-3 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 3/22 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 5 | 4 CASSLTGNTEAFF TRBV7-3 TRBD2 TRBJ1-1 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 2/22 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 6 | 5 CASSTRDPRQTQYF TRBV27 TRBD1 TRBJ2-5 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 1/22 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 7 | 6 CASSLWLPKETQYF TRBV5-1 TRBD1 TRBJ2-5 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 1/22 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 8 | 7 CASRKWNGELFF TRBV12-4 TRBD1 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 1/22 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 9 | 8 CSVEGPLAGEADTQYF TRBV29-1 TRBD2 TRBJ2-3 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 1/22 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 10 | 9 CASSPPGGRADTQYF TRBV11-3 TRBD2 TRBJ2-3 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 24/24 sanger CD8+ Japanese,HIV-1+ KI-112 TI8 PBMC HLA-B*51:01 11 | 10 CASAQGRGTEAFF TRBV27 TRBD1 TRBJ1-1 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 37/37 sanger CD8+ Japanese,HIV-1+ KI-124 TI8 PBMC HLA-B*51:01 12 | 11 CATDDDSARQLTF TRAV17 TRAJ22 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 15/15 sanger CD8+ Japanese,HIV-1+ KI-021 TI8 PBMC HLA-B*51:01 13 | 12 CATDEDSARQLTF TRAV17 TRAJ22 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 15/32 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 14 | 13 CATDDAGRRALTF TRAV17 TRAJ5 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 13/32 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 15 | 14 CAERTGGGNKLTF TRAV5 TRAJ10 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 4/32 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 16 | 15 CAAQRANRDDKIIF TRAV29/DV5 TRAJ30 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 22/22 sanger CD8+ Japanese,HIV-1+ KI-112 TI8 PBMC HLA-B*51:01 17 | 16 CAVSEGGATNKLIF TRAV8-6 TRAJ32 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 22/22 sanger CD8+ Japanese,HIV-1+ KI-124 TI8 PBMC HLA-B*51:01 18 | 17 CATDDDSARQLTF TRAV17 TRAJ22 CASSLTGGGELFF TRBV7-3 TRBD2 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 15/15 sanger CD8+ Japanese,HIV-1+ KI-021 TI8 cultured T-cells HLA-B*51:01 19 | 18 CATDDDSARQLTF TRAV17 TRAJ22 CASSLTGGGELFF TRBV7-3 TRBD2 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 3/3 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 cultured T-cells HLA-B*51:01 20 | 19 CVVSERAGGYQKV TRAV8-2 TRAJ13 CATSDLQGVRGVNEQF TRBV24-1 TRBD1 TRBJ2-1 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 7/7 sanger CD8+ Japanese,HIV-1+ KI-051 TI8 cultured T-cells HLA-B*51:01 21 | 20 CATDDDSARQLTF TRAV17 TRAJ22 CASSLTGGGKLFF TRBV7-3 TRBD1 TRBJ1-4 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 7/7 sanger CD8+ Japanese,HIV-1+ KI-112 TI8 cultured T-cells HLA-B*51:01 22 | 21 CAAQRANRDDKIIF TRAV29/DV5 TRAJ30 CASSPPGGRADTQYF TRBV11-3 TRBD2 TRBJ2-3 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 1/1 sanger CD8+ Japanese,HIV-1+ KI-112 TI8 cultured T-cells HLA-B*51:01 23 | 22 CAVSRGGSNYKLTF TRAV8-6 TRAJ53 CASSSGRGGEQYF TRBV27 TRBD2 TRBJ2-7 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 9/10 sanger CD8+ Japanese,HIV-1+ KI-124 TI8 cultured T-cells HLA-B*51:01 24 | 23 CAVSEGGATNKLIF TRAV8-6 TRAJ32 CASSSGRGGEQYF TRBV27 TRBD2 TRBJ2-7 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 1/10 sanger CD8+ Japanese,HIV-1+ KI-124 TI8 cultured T-cells HLA-B*51:01 25 | 24 CATDDDSARQLTF TRAV17 TRAJ22 CASSLTGGGKLFF TRBV7-3 TRBD1 TRBJ1-4 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 10/10 sanger CD8+ Japanese,HIV-1+ KI-127 TI8 cultured T-cells HLA-B*51:01 26 | 25 CATDDDSARQLTF TRAV17 TRAJ22 CASSLTGGGKLFF TRBV7-3 TRBD2 TRBJ1-4 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 10/10 sanger CD8+ Japanese,HIV-1+ KI-250 TI8 cultured T-cells HLA-B*51:01 27 | 26 CATDEAGRRALTF TRAV17 TRAJ5 CASSLTGGNTIYF TRBV7-3 TRBD1 TRBJ1-3 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 limiting-dilution-cloning,tetramer-sort 10/10 sanger CD8+ Japanese,HIV-1+ KI-391 TI8 cultured T-cells HLA-B*51:01 28 | 27 CATDDDSARQLTF TRAV17 TRAJ22 CASSLTGGGELFF TRBV7-3 TRBD2 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 22/25 yes sanger CD8+ Japanese,HIV-1+ KI-021 TI8 PBMC HLA-B*51:01 29 | 28 CAVTHHGQKLLF TRAV12-2 TRAJ16 CASSSNPIVPQETQYF TRBV28 TRBD2 TRBJ2-5 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 2/25 yes sanger CD8+ Japanese,HIV-1+ KI-021 TI8 PBMC HLA-B*51:01 30 | 29 CAVTHHGQKLLF TRAV12-2 TRAJ16 CASSRGAESYNSPLHF TRBV4-1 TRBD1 TRBJ1-6 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 1/25 yes sanger CD8+ Japanese,HIV-1+ KI-021 TI8 PBMC HLA-B*51:01 31 | 30 CATDEDSARQLTF TRAV17 TRAJ22 CASSLTGGGELFF TRBV7-3 TRBD2 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 8/18 yes sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 32 | 31 CATDVAGRRALTF TRAV17 TRAJ5 CASSSTGGNTIYF TRBV7-3 TRBD1 TRBJ1-3 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 2/18 yes sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 33 | 32 CATDEDSARQLTF TRAV17 TRAJ22 CASSLTGGARARLFF TRBV7-3 TRBD2 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 1/18 yes sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 34 | 33 CAERTGGGNKLTF TRAV5 TRAJ10 CASRKWNGELFF TRBV12-4 TRBD1 TRBJ2-2 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 5/18 yes sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 35 | 34 CAMRGPNRDDKIIF TRAV14/DV4 TRAJ30 CASSRRGEGHNEQFF TRBV11-3 TRBD2 TRBJ2-1 HomoSapiens HLA-B*51:01 B2M MHCI TAFTIPSI Pol HIV-1 PMID:24600035 tetramer-sort 2/18 yes sanger CD8+ Japanese,HIV-1+ KI-051 TI8 PBMC HLA-B*51:01 36 | -------------------------------------------------------------------------------- /chunks/PMID_24906112.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASSQEGGGQGQPQHF TRBV4-1 TRBJ1-5 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 60% sanger CD8+ N021 TL9 PBMC 3 | 2 CASSLATDGYTF TRBV5-6 TRBJ1-2 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 9.41% sanger CD8+ N021 TL9 PBMC 4 | 3 CASSQEGGGDGQPQHF TRBV4-1 TRBJ1-5 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 8.24% sanger CD8+ N021 TL9 PBMC 5 | 4 CASSFGLDEAFF TRBV12-3 TRBJ1-1 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 5.88% sanger CD8+ N021 TL9 PBMC 6 | 5 CASSQEGGGEGQPQHF TRBV4-1 TRBJ1-5 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 4.71% sanger CD8+ N021 TL9 PBMC 7 | 6 CASSFSKNTEAFF TRBV12-3 TRBJ1-1 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 3.53% sanger CD8+ N021 TL9 PBMC 8 | 7 CASSLEGTSGPQETQYF TRBV5-5 TRBJ2-5 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 2.35% sanger CD8+ N021 TL9 PBMC 9 | 8 CASSVGPNEQFF TRBV12-3 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 2.35% sanger CD8+ N021 TL9 PBMC 10 | 9 CASSQEGGGDGQPPHF TRBV4-1 TRBJ1-5 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 1.18% sanger CD8+ N021 TL9 PBMC 11 | 10 CASRQEGGGDGQPQHF TRBV4-1 TRBJ1-5 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 1.18% sanger CD8+ N021 TL9 PBMC 12 | 11 CAPTPEGGGQGQPQHF TRBV4-1 TRBJ1-5 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 1.18% sanger CD8+ N021 TL9 PBMC 13 | 12 CASSHLDSGLAVDTEAFF TRBV5-1 TRBJ1-1 HomoSapiens HLA-B*42:01 B2M MHCI FPRPWLHGL Vpr HIV PMID:24906112 tetramer-sort 40.26% sanger CD8+ N037 FL9 PBMC 14 | 13 CASSFRQGLGHTGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-B*42:01 B2M MHCI FPRPWLHGL Vpr HIV PMID:24906112 tetramer-sort 25.97% sanger CD8+ N037 FL9 PBMC 15 | 14 CASSLWSGASNEQFF TRBV7-2 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI FPRPWLHGL Vpr HIV PMID:24906112 tetramer-sort 24.68% sanger CD8+ N037 FL9 PBMC 16 | 15 CASSLYSGADQPQHF TRBV7-2 TRBJ1-5 HomoSapiens HLA-B*42:01 B2M MHCI FPRPWLHGL Vpr HIV PMID:24906112 tetramer-sort 7.79% sanger CD8+ N037 FL9 PBMC 17 | 16 CASSLWPGASNEQFF TRBV7-2 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI FPRPWLHGL Vpr HIV PMID:24906112 tetramer-sort 1.3% sanger CD8+ N037 FL9 PBMC 18 | 17 CASRTSGEETQYF TRBV6-2 TRBJ2-5 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 36.84% sanger CD8+ N052 IM9 PBMC 19 | 18 CASSVDKGGTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 34.21% sanger CD8+ N052 IM9 PBMC 20 | 19 CASSEDKGGGDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 7.89% sanger CD8+ N052 IM9 PBMC 21 | 20 CASSVDKGGVDEQFF TRBV9 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 6.58% sanger CD8+ N052 IM9 PBMC 22 | 21 CASGDSGDEQFF TRBV5-1 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 5.26% sanger CD8+ N052 IM9 PBMC 23 | 22 CASRTSGDYEQYF TRBV6-2 TRBJ2-7 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 3.95% sanger CD8+ N052 IM9 PBMC 24 | 23 CASSFLTGARSKNIQYF TRBV5-4 TRBJ2-4 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.32% sanger CD8+ N052 IM9 PBMC 25 | 24 CASSVDKGGPDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.32% sanger CD8+ N052 IM9 PBMC 26 | 25 CASSEDKGGADTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.32% sanger CD8+ N052 IM9 PBMC 27 | 26 CASRTGGEETQYF TRBV6-2 TRBJ2-5 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.32% sanger CD8+ N052 IM9 PBMC 28 | 27 CASSLVFGTAGGQQFF TRBV5-5 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 63.1% sanger CD8+ N106 TL9 PBMC 29 | 28 CASSFSKNTEAFF TRBV12-3 TRBJ1-1 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 33.33% sanger CD8+ N106 TL9 PBMC 30 | 29 CASSWTETGELFF TRBV6-5 TRBJ2-2 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 2.38% sanger CD8+ N106 TL9 PBMC 31 | 30 CTSSLVFGTAGGRQFF TRBV5-5 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI TPQDLNTML p24 HIV PMID:24906112 tetramer-sort 1.19% sanger CD8+ N106 TL9 PBMC 32 | 31 CASRTSGEETQYF TRBV6-2 TRBJ2-5 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 36.84% sanger CD8+ N052 IM9 PBMC 33 | 32 CASSVDKGGTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 34.21% sanger CD8+ N052 IM9 PBMC 34 | 33 CASSEDKGGGDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 7.89% sanger CD8+ N052 IM9 PBMC 35 | 34 CASSVDKGGVDEQFF TRBV9 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 6.58% sanger CD8+ N052 IM9 PBMC 36 | 35 CASGDSGDEQFF TRBV5-1 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 5.26% sanger CD8+ N052 IM9 PBMC 37 | 36 CASRTSGDYEQYF TRBV6-2 TRBJ2-7 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 3.95% sanger CD8+ N052 IM9 PBMC 38 | 37 CASSFLTGARSKNIQYF TRBV5-4 TRBJ2-4 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.32% sanger CD8+ N052 IM9 PBMC 39 | 38 CASSVDKGGPDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.32% sanger CD8+ N052 IM9 PBMC 40 | 39 CASSEDKGGADTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.32% sanger CD8+ N052 IM9 PBMC 41 | 40 CASRTGGEETQYF TRBV6-2 TRBJ2-5 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.32% sanger CD8+ N052 IM9 PBMC 42 | 41 CASRGTGVHEQYF TRBV6-2 TRBJ2-7 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 56.96% sanger CD8+ N033 IM9 PBMC 43 | 42 CASSVDKGGADTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 29.11% sanger CD8+ N033 IM9 PBMC 44 | 43 CASRTSGGHEQFF TRBV6-2 TRBJ2-1 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 12.66% sanger CD8+ N033 IM9 PBMC 45 | 44 CASSLDPRMNTEAFF TRBV11-2 TRBJ1-1 HomoSapiens HLA-B*42:01 B2M MHCI IIKDYGKQM Int HIV PMID:24906112 tetramer-sort 1.27% sanger CD8+ N033 IM9 PBMC 46 | 45 CASSQDRLVNADTQYF TRBV4-2 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI RPGGKKHYM Nef HIV PMID:24906112 tetramer-sort 56.67% sanger CD8+ R019 RM9 PBMC 47 | 46 CASSLAGDRGNYGYTF TRBV27 TRBJ1-2 HomoSapiens HLA-B*42:01 B2M MHCI RPGGKKHYM Nef HIV PMID:24906112 tetramer-sort 31.11% sanger CD8+ R019 RM9 PBMC 48 | 47 CASRRQGALNTEAFF TRBV27 TRBJ1-1 HomoSapiens HLA-B*42:01 B2M MHCI RPGGKKHYM Nef HIV PMID:24906112 tetramer-sort 10% sanger CD8+ R019 RM9 PBMC 49 | 48 CASSQDRVVGADTQYF TRBV4-2 TRBJ2-3 HomoSapiens HLA-B*42:01 B2M MHCI RPGGKKHYM Nef HIV PMID:24906112 tetramer-sort 1.11% sanger CD8+ R019 RM9 PBMC 50 | 49 CASSQDPFSVGELFF TRBV4-2 TRBJ2-2 HomoSapiens HLA-B*42:01 B2M MHCI RPGGKKHYM Nef HIV PMID:24906112 tetramer-sort 1.11% sanger CD8+ R019 RM9 PBMC -------------------------------------------------------------------------------- /chunks/PMID_25157096.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAVQAGGNNRLAF TRAV20*02 TRAJ7*01 CASSLERDGYTF TRBV5-1*01 TRBD1*01 TRBJ1-2*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII VELGGGPGA INS HomoSapiens PMID:25157096 antigen-expressing-targets no RNA-seq Type 1 Diabetes TCL 3 | 2 CIAIYNFNKFYF TRAV26-1*01 TRAJ21*01 CASSLEASSYNSPLHF TRBV5-1*01 TRBD2*01 TRBJ1-6*02 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII VELGGGPGA INS HomoSapiens PMID:25157096 antigen-expressing-targets no RNA-seq Type 1 Diabetes TCL 4 | 3 CIVSHNAGNMLTF TRAV26-1*01 TRAJ39*01 CASSLERETQYF TRBV5-1*01 TRBD2*01 TRBJ2-5*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII VELGGGPGA INS HomoSapiens PMID:25157096 antigen-expressing-targets no RNA-seq Type 1 Diabetes TCL 5 | 4 CALKYGANNLFF TRAV6*02 TRAJ36*01 CASSPTTGGDEAFF TRBV18*01 TRBD1*01 TRBJ1-1*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII QVELGGGPGAG INS HomoSapiens PMID:25157096 antigen-expressing-targets no RNA-seq Type 1 Diabetes TCL 6 | 5 CIVRVEIQGAQKLVF TRAV26-1*01 TRAJ54*01 CASSLGPGQRETQYF TRBV5-1*01 TRBD1*01 TRBJ2-5*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII QVELGGGPG INS HomoSapiens PMID:25157096 antigen-expressing-targets no RNA-seq Type 1 Diabetes TCL 7 | 6 CAGGFSDGQKLLF TRAV25*01 TRAJ16*01 CSARTEAYEQYF TRBV20-1*03 TRBD1*01 TRBJ2-7*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII AGSLQPLALE INS HomoSapiens PMID:25157096 antigen-expressing-targets no RNA-seq Type 1 Diabetes TCL 8 | 7 CALSRAGTGNQFYF TRAV20*02 TRAJ58*01 CSARDQQRVDTQYF TRBV20-1*01 TRBD2*01 TRBJ2–3*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII AGSLQPLAL INS HomoSapiens PMID:25157096 antigen-expressing-targets no RNA-seq Type 1 Diabetes TCL -------------------------------------------------------------------------------- /chunks/PMID_28623251.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAETPTNDYKLSF TRAV5*01 TRAJ20*01 CASSSETELLYYGYTF TRBV6-6*02 TRBJ1-2*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 5.1% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V001 PBMC 3 | 2 SSGNQFYF TRAV21*01 TRAJ49*01 CASSQQTGTIGGYTF TRBV6-5*01 TRBJ1-2*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 67.5% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V001 PBMC 4 | 3 CADYYGQNFVF TRAV3*01 TRAJ26*01 CASSFQGFTEAFF TRBV28*01 TRBJ1-1*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 27.4% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V001 PBMC 5 | 4 CASPTGNQFYF TRAV24*01 TRAJ49*01 CASSFTLGTGGVEQYF TRBV27*01 TRBJ2-7*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 10.3% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V004 PBMC 6 | 5 CAEIPSNDYKLSF TRAV5*01 TRAJ20*01 CSARGQDIYEQYF TRBV20-1*01 TRBJ2-7*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 6.9% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V004 PBMC 7 | 6 CASGSQGNLIF TRAV3*01 TRAJ42*01 CASGLTGFMDEQYF TRBV25-1*01 TRBJ2-7*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 6.9% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V004 PBMC 8 | 7 CAGLTTDSWGKFQF TRAV25*01 TRAJ24*01 CASSVDVAGGYNEQFF TRBV7-3*01 TRBJ2-1*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 3.45% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V004 PBMC 9 | 8 CATYLTGNQFYF TRAV12-3*01 TRAJ49*01 CASSQALPYEQYF TRBV12-4*01 TRBJ2-7*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 55.2% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V004 PBMC 10 | 9 CAVCNFNKFYF TRAV24*01 TRAJ21*01 CASSITLGTGGVEQYF TRBV27*01 TRBJ2-7*01 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:28623251 tetramer-sort 17.2% yes sanger antigen-loaded-targets CD8+ healthy,CMV-seropositive V004 PBMC 11 | -------------------------------------------------------------------------------- /chunks/PMID_29429978.txt: -------------------------------------------------------------------------------- 1 | chunk.id v.alpha j.alpha cdr3.alpha v.beta d.beta j.beta cdr3.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 TRAV17*01 TRAJ36*01 CAVTGANNLFF TRBV19*01 TRBD1*01 TRBJ2-2*01 CASSIEGPTGELF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Type1 Diabetes D222D clones1,2,3 3 | 2 TRAV35*02 TRAJ36*01 CAGTRNNLFF TRBV19*01 TRBD2*01 TRBJ2-7*01 CASGGSSYEQYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Type1 Diabetes D010R clone1E2 4 | 3 TRAV25*01 TRAJ20*01 CAGGSNDYKLSF TRBV6-1*01 TRBD1*01 TRBJ2-3*01 CASSSVGVDTQYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Type1 Diabetes D010R clone1D3 5 | 4 TRAV19*01 TRAJ23*01 CALSEATYNQGGKLIF TRBV19*01 TRBJ1-3*01 CASSIFPNPGNTIYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Type1 Diabetes D267 33B8 6 | 5 TRAV14/DV4*03 TRAJ9*01 CAMREGLTGGFKTIF TRBV11-2*01 TRBD1*01 TRBJ1-1*01 CASSPFLTGSNTEAFF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Type1 Diabetes D349 178B9 7 | 6 TRAV19*01 TRAJ20*01 CALSPAETSDYKLSF TRBV19*01 TRBD1*01 TRBJ1-1*01 CASTLTGFAEAFF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Type1 Diabetes D351D 188D3 8 | 7 TRAV39*01 TRAJ29*01 CAVDMGNTPLVF TRBV7-2*02 TRBD1*01 TRBJ2-3*01 CASSPSWLSGVTQYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H017N CloneA1 9 | 8 TRAV38-2/DV8*01 TRAJ41*01 CALRSGYALNF TRBV25-1*01 TRBJ2-5*01 CASSDQETQYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H034O 141B9 10 | 9 TRAV3*01 TRAJ39*01 CAVRDIFNAGNMLTF TRBV19*01 TRBJ2-1*01 CASSIVSSSYNEQFF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H079O 42D8 11 | 10 TRAV38-1*01 TRAJ45*01 CAFYSGGGADGLTF TRBV27*01 TRBD1*01 TRBJ2-3*01 CASRAGSFSTDTQYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H087N 157C3 12 | 11 TRAV29/DV5*01 TRAJ40*01 CAASGTLTTSGTYKYIF TRBV4-2*01 TRBD1*01 TRBJ2-7*01 CASSQEGTAYEQYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H328C Clone8E8 13 | 12 TRAV21*01 TRAJ57*01 CAVVRTQGGSEKLVF TRBV9*01 TRBD1*01 TRBJ1-6*01 CASSPWTGIPYNSPLHF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H328C Clone9B3 14 | 13 TRAV25*01 TRAJ26*01 CAGILSYGQNFVF TRBV25-1*01 TRBD1*01 TRBJ1-2*01 CASSEVGQGFNGYTF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H328C Clone9C8 15 | 14 TRAV40*01 TRAJ47*02 CLLMEYGNKLVF TRBV6-5*01 TRBD1*01 TRBJ2-7*01 CASQSYRVGSEQYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H314C Clone6C4 16 | 15 TRAV38-2/DV8*01 TRAJ26*01 CAFFPYGQNFVF TRBV6-5*01 TRBD1*01 TRBJ2-7*01 CASQSYRVGSEQYF HomoSapiens HLA-A*02 B2M MHCI VAANIVLTV SLC30A8 HomoSapiens PMID:29429978 cultured-T-cells sanger antigen-expressing-targets Healthy H314C Clone6C4 17 | -------------------------------------------------------------------------------- /chunks/PMID_29752423.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAAGGNYKPTF TRAV14-1 TRAJ6 CASSRANYEQYF TRBV12-1 TRBD2 TRBJ2-7 MusMusculus H-2KB B2M MHCI SIINFEKL OVA GallusGallus PMID:29752423 tetramer-sort 0.371428571 sanger tetramer-stain,antigen-loaded-targets,antigen-expressing-targets CD8+Kb-OVA+ 1 healthy V14-c1 LN,spleen 3 | 2 CASGGNYKPTF TRAV14-1 TRAJ6 CASSRANYEQYF TRBV12-1 TRBD2 TRBJ2-7 MusMusculus H-2KB B2M MHCI SIINFEKL OVA GallusGallus PMID:29752423 tetramer-sort 0.164285714 sanger tetramer-stain,antigen-loaded-targets,antigen-expressing-targets CD8+Kb-OVA+ 1 healthy V14-c2 LN,spleen 4 | 3 CAAGDNNRIFF TRAV14-1 TRAJ31 CASSRANYEQYF TRBV12-1 TRBD2 TRBJ2-7 MusMusculus H-2KB B2M MHCI SIINFEKL OVA GallusGallus PMID:29752423 tetramer-sort 0.05 sanger tetramer-stain,antigen-loaded-targets,antigen-expressing-targets CD8+Kb-OVA+ 1 healthy V14-c7 LN,spleen 5 | 4 CAAGDTNKVVF TRAV14-1 TRAJ34 CASSRANYEQYF TRBV12-1 TRBD2 TRBJ2-7 MusMusculus H-2KB B2M MHCI SIINFEKL OVA GallusGallus PMID:29752423 tetramer-sort 0.042857143 sanger tetramer-stain,antigen-loaded-targets,antigen-expressing-targets CD8+Kb-OVA+ 1 healthy V14c-8 LN,spleen 6 | 5 CAGGGNYKPTF TRAV14-1 TRAJ6 CASSRANYEQYF TRBV12-1 TRBD2 TRBJ2-7 MusMusculus H-2KB B2M MHCI SIINFEKL OVA GallusGallus PMID:29752423 tetramer-sort 0.014285714 sanger tetramer-stain,antigen-loaded-targets,antigen-expressing-targets CD8+Kb-OVA+ 1 healthy V14-c12 LN,spleen 7 | 6 CAASDDNRIFF TRAV14-1 TRAJ31 CASSRANYEQYF TRBV12-1 TRBD2 TRBJ2-7 MusMusculus H-2KB B2M MHCI SIINFEKL OVA GallusGallus PMID:29752423 tetramer-sort 0.014285714 sanger tetramer-stain,antigen-loaded-targets,antigen-expressing-targets CD8+Kb-OVA+ 1 healthy V14-c17 LN,spleen 8 | -------------------------------------------------------------------------------- /chunks/PMID_34433824.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAVQAGGNNRLAF TRAV20*2 TRAJ7*01 CASSLERDGYTF TRBV5-1*01 TRBD1*01 TRBJ1-2*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 A1.9 6XCO 3 | 2 CAFFGQGAQKLVF TRAV38-1*03 TRAJ54*01 CASSLSASGGATDTQYF TRBV5-1*01 TRBD2*01 TRBJ2-3*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 A3.10 6XC9 4 | 3 CIVRDSNYQLIW TRAV26-1 TRAJ33*01 CSANRDGGGYTF TRBV29-1 TRBD1*01 TRBJ1-2*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 7/19 ET600-1 PBMC 5 | 4 CAVGGTSGSARQLTF TRAV8-3 TRAJ22*01 CAISEGERGSNYGYTF TRBV10-3 TRBD2*01 TRBJ1-2*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 6/19 ET600-2 PBMC 6 | 5 CAVGFNAGKSTF TRAV8-3 TRAJ27*01 CASSLGPTGTNTEAFF TRBV5-1 TRBD1*01 TRBJ1-1*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/19 ET600-3 PBMC 7 | 6 CAMRPNNAGNMLTF TRAV14/DV4 TRAJ39*01 CATSRGNQGPNQPQHF TRBV15 TRBD1*01 TRBJ1-5*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/19 ET600-4 PBMC 8 | 7 CIVRVNNAGNMLTF TRAV26-1 TRAJ39*01 CASSRLDNGYTF TRBV28 TRBD2*01 TRBJ1-2*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/19 ET600-5 PBMC 9 | 8 CAVNQAGTALIF TRAV12-2 TRAJ15*01 CASSWAYNEQFF TRBV11-1 TRBD1*01 TRBJ2-1*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/19 ET600-6 PBMC 10 | 9 CAVRDGGSYIPTF TRAV3 TRAJ6*01 CASSLLPDRGHEQYF TRBV7-8 TRBD1*01 TRBJ2-7*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/19 ET600-7 PBMC 11 | 10 CALSEVNTGGFKTIF TRAV19 TRAJ9*01 CAISLQGSRSGANVLTF TRBV10-3 TRBD1*01 TRBJ2-6*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/19 ET600-8 PBMC 12 | 11 CIVRVEIQGAQKLVF TRAV26-1 TRAJ54*01 CASSLGPGLRETQYF TRBV5-1 TRBD1*01 TRBJ2-5*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 4/14 ET650-1 PBMC 13 | 12 CIVRVGYNAGNMLTF TRAV26-1 TRAJ39*01 CSAIAGPNQPQHF TRBV20-1 TRBD2*01 TRBJ1-5*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 3/14 ET650-2 PBMC 14 | 13 CIVRPQKGGSQGNLIF TRAV26-1 TRAJ42*01 CASSHHSTDTQYF TRBV3-1 TRBJ2-3*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 2/14 ET650-3 PBMC 15 | 14 CIVRVAIEGSQGNLIF TRAV26-1 TRAJ42*01 CASSLRRGDTIYF TRBV5-1 TRBD1*01 TRBJ1-3*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/14 ET650-4 PBMC 16 | 15 CIVRLQSGGFKTIF TRAV26-1 TRAJ9*01 CSAYSPGDRDFSNYGYTF TRBV20-1 TRBD1*01 TRBJ1-2*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/14 ET650-5 PBMC 17 | 16 CAVDIQGAQKLVF TRAV39 TRAJ54*01 CASSLRTAISRTDTQYF TRBV7-8 TRBD1*01 TRBJ2-3*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/14 ET650-6 PBMC 18 | 17 CGTLAFGNEKLTF TRAV30 TRAJ48*01 CASHRGKGNSPLHF TRBV19 TRBD2*01 TRBJ1-6*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/14 ET650-7 PBMC 19 | 18 CAGQLWNTGNQFYF TRAV35 TRAJ49*01 SHLRGASTDTQ TRBV11-1 TRBD2*01 TRBJ2-3*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/14 ET650-8 PBMC 20 | 19 CAVNHGNEKLTF TRAV12-2 TRAJ48*01 CASSPWEGRMDTEAFF TRBV18 TRBD1*01 TRBJ1-1*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 18/19 ET672-1 PBMC 21 | 20 CVVVSNTGKLIF TRAV12-1 TRAJ37*02 CASSQWVSGEDEQFF TRBV23-1 TRBD2*01 TRBJ2-1*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID: 34433824 tetramer-sort amplicon-seq 1/19 ET672-2 PBMC -------------------------------------------------------------------------------- /chunks/PMID_35314848.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAYRSVPKVSGSRLTF TRAV38-2/DV8*01 TRAJ53 CASSLRGGQSYEQYF TRBV12-4*01 TRBJ2-7 HomoSapiens HLA-A*02:01 B2M MHCI MLYQHLLPL INS-DRiP HomoSapiens PMID:34811538 tetramer-sort yes amplicon-seq antigen-loaded-targets CD8+ PBMC 3 | 2 CAVSGNTGKLIF TRAV20*01 TRAJ37 CASSQWDNQPQHF TRBV4-1*01 TRBJ1-5 HomoSapiens HLA-B*08:01 B2M MHCI WMRLLPLL INS HomoSapiens PMID:34811538 tetramer-sort yes amplicon-seq antigen-loaded-targets CD8+ PBMC 4 | 3 CAASLKTSYDKVIF TRAV23/DV6*01 TRAJ50 CAISEGAPNTEAFF TRBV10-3*01 TRBJ1-1 HomoSapiens HLA-A*01:01 B2M MHCI FGDHPGHSY PTPRN HomoSapiens PMID:34811538 tetramer-sort yes amplicon-seq antigen-loaded-targets CD8+ PBMC 5 | 4 CAESTSGGKLIF TRAV5*01 TRAJ37 CSVGTGGTNEKLFF TRBV29-1*01 TRBJ1-4 HomoSapiens HLA-A*02:01 B2M MHCI GLCTLVAML BLMF1 EBV PMID:34811538 tetramer-sort yes amplicon-seq antigen-loaded-targets CD8+ PBMC 6 | 5 CVVNGKDSSYKLIF TRAV12-1*01 TRAJ12 CASSGGAVAPSEQFF TRBV2*01 TRBJ2-1 HomoSapiens HLA-A*02:01 B2M MHCI GLCTLVAML BLMF1 EBV PMID:34811538 tetramer-sort yes amplicon-seq antigen-loaded-targets CD8+ PBMC 7 | 6 CSARRGTEAFF TRBV20 TRBJ1-1 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 8 | 7 CATSAPDRGNNQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 9 | 8 CATSDFRVGDNQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 10 | 9 CATSDPDRGDNQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 11 | 10 CATSDPGQGDHQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 12 | 11 CATSDPGQGNNQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 13 | 12 CATSDPRQGDNQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 14 | 13 CATSDPRTGDNQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 15 | 14 CATSDPRVGDNQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 16 | 15 CATSDPSRGDNQPQHF TRBV24 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 17 | 16 CATSDVSGGNYNEQFF TRBV24 TRBJ2-1 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 18 | 17 CASSEGASNQPQHF TRBV6-1 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC 19 | 18 CASSEGVSNQPQHF TRBV6-1 TRBJ1-5 HomoSapiens HLA-DRA*01:01 HLA-DRB1*15:01 MHCII NLLLQYGSFCTQLNRAL Spike SARS-CoV-2 PMID:35314848 tetramer-sort yes amplicon-seq CD4+ PBMC -------------------------------------------------------------------------------- /chunks/PMID_35525797.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAESYTGGFKTIF TRAV5*01 TRAJ9*01 CASGTEAFF TRBV6-1*01 TRBJ1-1*01 HomoSapiens HLA-B*35:01 B2M MHCI HPVGEADYFEY EBNA1 EBV PMID:35525797 tetramer-sort 54/87 yes illumina antigen-loaded-targets HPV13A10 CD8+ 62 EBV-seropositive,healthy G1 HPV13A10 HPV stem-cell-graft,TCL HLA-B*35:01 3 | 2 CVVSEEGGFKTIF TRAV10*01 TRAJ9*01 CASGLGGSNEQFF TRBV12-5*01 TRBJ2-1*01 HomoSapiens HLA-B*35:01 B2M MHCI HPVGEADYFEY EBNA1 EBV PMID:35525797 tetramer-sort 11/87 yes illumina antigen-loaded-targets HPV13B12 CD8+ 13 EBV-seropositive,healthy G1 HPV13B12 HPV stem-cell-graft,TCL HLA-B*35:01 4 | 3 CAVQELVTSGSRLTF TRAV20*01 TRAJ58*01 CASTGAGEGPFF TRBV9*01 TRBJ1-1*01 HomoSapiens HLA-B*35:01 B2M MHCI HPVGEADYFEY EBNA1 EBV PMID:35525797 tetramer-sort 17/98 yes illumina antigen-loaded-targets HPV9A2 CD8+ 17 EBV-seropositive,healthy G3 HPV9A2 HPV stem-cell-graft,TCL HLA-B*35:01 5 | 4 CAVQAMTSSNYKLTF TRAV20*01 TRAJ53*01 CASSARTGELFF TRBV9*01 TRBJ2-2*01 HomoSapiens HLA-B*35:01 B2M MHCI HPVGEADYFEY EBNA1 EBV PMID:35525797 tetramer-sort 6/98 yes illumina antigen-loaded-targets HPV9C10 CD8+ 6 EBV-seropositive,healthy G3 HPV9C10 HPV stem-cell-graft,TCL HLA-B*35:01 6 | 5 CALSEAGGFGNEKLTF TRAV19*01 TRAJ48*01 CAISDPRDSYEQYF TRBV10-3*1 TRBJ2-7*01 HomoSapiens HLA-B*35:01 B2M MHCI YPLHEQHGM EBNA3A EBV PMID:35525797 tetramer-sort 9/143 yes illumina antigen-loaded-targets YPL3D3 CD8+ 6 EBV-seropositive,healthy G2 YPL3D3 YPL stem-cell-graft,TCL HLA-B*35:01 7 | 6 CAVMSSGGSYIPTF TRAV1-2*01 TRAJ6*01 CAISTGDSNQPQHF TRBV10-3*1 TRBJ1-5*01 HomoSapiens HLA-B*35:01 B2M MHCI EPLPQGQLTAY BZLF1 EBV PMID:35525797 tetramer-sort 21/175 yes illumina antigen-loaded-targets EPL11A7 CD8+ 12 EBV-seropositive,healthy G1 EPL11A7 EPL stem-cell-graft,TCL HLA-B*35:01 8 | 7 CAFPGGNKLVF TRAV24*01 TRAJ47*01 CAISEWDSPTLNSPLHF TRBV10-3*1 TRBJ1-6*01 HomoSapiens HLA-B*35:01 B2M MHCI EPLPQGQLTAY BZLF1 EBV PMID:35525797 tetramer-sort 16/175 yes illumina antigen-loaded-targets EPL11A12 CD8+ 9 EBV-seropositive,healthy G1 EPL11A12 EPL stem-cell-graft,TCL HLA-B*35:01 9 | 8 CAVRGSGGSYIPTF TRAV1-2*01 TRAJ6*01 CATGTGDSNQPQHF TRBV10-3*1 TRBJ1-5*01 HomoSapiens HLA-B*35:01 B2M MHCI EPLPQGQLTAY BZLF1 EBV PMID:35525797 tetramer-sort 9/127 yes illumina antigen-loaded-targets EPL7A10 CD8+ 7 EBV-seropositive,healthy G3 EPL7A10 EPL stem-cell-graft,TCL HLA-B*35:01 10 | 9 CALNAGGTSYGKLTF TRAV24*01 TRAJ52*01 CASSRDFYAYNEQFF TRBV7-3*01 TRBJ2-1*01 HomoSapiens HLA-B*35:01 B2M MHCI EPLPQGQLTAY BZLF1 EBV PMID:35525797 tetramer-sort 115/129 yes illumina antigen-loaded-targets EPL11A10 CD8+ 89 EBV-seropositive,healthy G4 EPL11A10 EPL stem-cell-graft,TCL HLA-B*35:01 11 | 10 CAVEDMNSGGYQKVTF TRAV2*01 TRAJ13*02 CASKRTATYEQYF TRBV28*01 TRBJ2-7*01 HomoSapiens HLA-B*35:01 B2M MHCI EPLPQGQLTAY BZLF1 EBV PMID:35525797 tetramer-sort 9/157 yes illumina antigen-loaded-targets EPL13B9 CD8+ 6 EBV-seropositive,healthy G5 EPL13B9 EPL stem-cell-graft,TCL HLA-B*35:01 12 | 11 CAESTGKLIF TRAV5*01 TRAJ37*01 CSVGTGGTNEKLFF TRBV29-1*01 TRBJ1-4*01 HomoSapiens HLA-A*02:01 B2M MHCI GLCTLVAML BMLF1 EBV PMID:35525797 tetramer-sort 8/88 yes illumina antigen-loaded-targets GLC1B11 CD8+ 9 EBV-seropositive,healthy G6 GLC1B11 GLC stem-cell-graft,TCL HLA-A*02:01 13 | 12 CAESTSWGKLQF TRAV5*01 TRAJ24*02 CSVGTGGTNEKLFF TRBV29-1*01 TRBJ1-4*01 HomoSapiens HLA-A*02:01 B2M MHCI GLCTLVAML BMLF1 EBV PMID:35525797 tetramer-sort 3/88 yes illumina antigen-loaded-targets GLC1B4 CD8+ 3 EBV-seropositive,healthy G6 GLC1B4 GLC stem-cell-graft,TCL HLA-A*02:01 14 | 13 CAILMDSNYQLIW TRAV21*01 TRAJ33*01 CASSEDGMNTEAFF TRBV10-2*02 TRBJ1-1*01 HomoSapiens HLA-A*02:01 B2M MHCI CLGGLLTMV LMP2A EBV PMID:35525797 tetramer-sort 26/46 yes illumina antigen-loaded-targets CLG3A10 CD8+ 57 EBV-seropositive,healthy G6 CLG3A10 CLG stem-cell-graft,TCL HLA-A*02:01 15 | 14 CATEGDSGYSTLTF TRAV17*01 TRAJ11*01 CASSYQGGNYGYTF TRBV6-5*01 TRBJ1-2*01 HomoSapiens HLA-A*02:01 B2M MHCI FLYALALLL LMP2A EBV PMID:35525797 tetramer-sort 13/70 yes illumina antigen-loaded-targets FLY5D11 CD8+ 19 EBV-seropositive,healthy G6 FLY5D11 FLY stem-cell-graft,TCL HLA-A*02:01 16 | 15 CATVGNSGYSTLTF TRAV17*01 TRAJ11*01 CASSKQGGNIQYF TRBV6-5*01 TRBJ2-4*01 HomoSapiens HLA-A*02:01 B2M MHCI FLYALALLL LMP2A EBV PMID:35525797 tetramer-sort 11/70 yes illumina antigen-loaded-targets FLY5B5 CD8+ 16 EBV-seropositive,healthy G6 FLY5B5 FLY stem-cell-graft,TCL HLA-A*02:01 17 | 16 CAYRSAFKLTF TRAV38-2/DV8*01 TRAJ48*01 CAWSVPLGRREKLFF TRBV30*01 TRBJ1-4*01 HomoSapiens HLA-A*02:01 B2M MHCI YVLDHLIVV BRLF1 EBV PMID:35525797 tetramer-sort 2/26 yes illumina antigen-loaded-targets YVL16D1 CD8+ 8 EBV-seropositive,healthy G6 YVL16D1 YVL stem-cell-graft,TCL HLA-A*02:01 -------------------------------------------------------------------------------- /chunks/PMID_36477533.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAVSLGTGAGSYQLTF TRAV21 TRAJ28 CASSVGLYSTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*27:05 B2M MHCI TRLALIAPK PRPF3 HomoSapiens PMID:36477533 antigen-loaded-targets yes amplicon-seq tetramer-stain Ankylosing Spondylitis AS3.1 synovial fluid 7n2s 3 | 2 CAVLSPVQETSGSRLTF TRAV21 TRAJ58 CASSVGLFSTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*27:05 B2M MHCI TRLALIAPK PRPF3 HomoSapiens PMID:36477533 antigen-loaded-targets yes amplicon-seq tetramer-stain Ankylosing Spondylitis AS4.2 synovial fluid 7n2n 4 | 3 CAVLSPVQETSGSRLTF TRAV21 TRAJ58 CASSVGLFSTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*27:05 B2M MHCI LRVMMLAPF YEIH E.Coli PMID:36477533 antigen-loaded-targets yes amplicon-seq tetramer-stain Ankylosing Spondylitis AS4.2 synovial fluid 7n2o 5 | 4 CAVSNFNKFYF TRAV21 TRAJ21 CASSVATYSTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*27:05 B2M MHCI TRLALIAPK PRPF3 HomoSapiens PMID:36477533 antigen-loaded-targets yes amplicon-seq tetramer-stain Ankylosing Spondylitis AS4.3 synovial fluid 7n2r 6 | 5 CAVSNFNKFYF TRAV21 TRAJ21 CASSVATYSTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*27:05 B2M MHCI GQVMVVAPR RNASEH2B HomoSapiens PMID:36477533 antigen-loaded-targets yes amplicon-seq tetramer-stain Ankylosing Spondylitis AS4.3 synovial fluid 7n2p 7 | 6 CAVSNFNKFYF TRAV21 TRAJ21 CASSVATYSTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*27:05 B2M MHCI LRVMMLAPF YEIH E.Coli PMID:36477533 antigen-loaded-targets yes amplicon-seq tetramer-stain Ankylosing Spondylitis AS4.3 synovial fluid 7n2q 8 | 7 CAVNSPGSGAGSYQLTF TRAV21 TRAJ28 CASSVGTYSTDTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-B*27:05 B2M MHCI LRVMMLAPF YEIH E.Coli PMID:36477533 antigen-loaded-targets yes amplicon-seq tetramer-stain Ankylosing Spondylitis AS8.4 synovial fluid 8cx4 9 | -------------------------------------------------------------------------------- /chunks/PMID_37418020.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id comment 2 | 1 CAVGDTGGFKTIF TRAV8-3*01 TRAJ9*01 CASSFPGGNTGELFF TRBV7-9*03 TRBD2*02 TRBJ2-2*01 HomoSapiens DPA1*02:02 DPB1*05:01 MHCII DKSMKVTVAFNQF pCj1 CryptomeriaJaponica PMID:37418020 antigen-loaded-targets amplicon-seq Th2 PBMC 3 | 2 CAVAPTYNTDKLIF TRAV8-3*01 TRAJ34*01 CASSSKGGAGELFF TRBV7-9*03 TRBD2*01 TRBJ2-2*01 HomoSapiens DPA1*02:02 DPB1*05:01 MHCII DKSMKVTVAFNQF pCj1 CryptomeriaJaponica PMID:37418020 antigen-loaded-targets amplicon-seq Th2 PBMC 4 | 3 CALRSNFGNEKLTF TRAV16*01 TRAJ48*01 CASSLVVAGVYTGELFF TRBV5-1*01 TRBD2*02 TRBJ2-2*01 HomoSapiens DPA1*02:02 DPB1*05:01 MHCII DKSMKVTVAFNQF pCj1 CryptomeriaJaponica PMID:37418020 antigen-loaded-targets amplicon-seq Th2 PBMC 5 | 4 CGANAGKSTF TRAV12-3*01 TRAJ27*01 CAWSVMVWGSEGEQYF TRBV30*01 TRBD2*02 TRBJ2-7*01 HomoSapiens DPA1*02:02 DPB1*05:01 MHCII DKSMKVTVAFNQF pCj1 CryptomeriaJaponica PMID:37418020 antigen-loaded-targets amplicon-seq Th2 PBMC -------------------------------------------------------------------------------- /chunks/PMID_38508137.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CALDMFSGGYNKLIF TRAV16 TRAJ4 CATSRVKTSGGYEQYF TRBV15 TRBJ2-7 HomoSapiens HLA-A*68:02 B2M MHCI EIFDRYGEEV DNAJB1-PRKACA HomoSapiens PMID:38508137 tetramer-sort yes amplicon-seq CD8+ 1/2 Fibrolamellar carcinoma 3 | 2 CAVNVFPGNQFYF TRAV12-2 TRAJ49 CASSLGQTYEQYF TRBV5-4 TRBJ2-7 HomoSapiens HLA-A*68:02 B2M MHCI EIFDRYGEEV DNAJB1-PRKACA HomoSapiens PMID:38508137 tetramer-sort yes amplicon-seq CD8+ 1/2 Fibrolamellar carcinoma 4 | -------------------------------------------------------------------------------- /chunks/PMID_39043656.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id comment 2 | 1 CALGDSNYQL TRAV6-6 TRAJ33 CAACGAGGAGQNTL TRBV13-2 TRBD2 TRBJ2-4 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII GVYATXSSAVRLR VIM HomoSapiens PMID:39043656 tetramer-sort 1/32 PCR CD4+ x for citrulline 3 | 2 CALGDHSGSWQL TRAV6-6 TRAJ22 CASSLRTGANSDY TRBV19 TRBD1 TRBJ1-2 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII GVYATXSSAVRLR VIM HomoSapiens PMID:39043656 tetramer-sort 20/32 PCR CD4+ x for citrulline 4 | 3 CALGDTGNYKY TRAV6-6 TRAJ40 CASSGHNSGNTL TRBV13-3 TRBD1 TRBJ1-3 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII GVYATXSSAVRLR VIM HomoSapiens PMID:39043656 tetramer-sort 1/32 PCR CD4+ x for citrulline 5 | 4 CALGDTGNYKY TRAV6-6 TRAJ40 CASSAVNSGNTL TRBV13-3 TRBD1 TRBJ1-3 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII GVYATXSSAVRLR VIM HomoSapiens PMID:39043656 tetramer-sort 9/32 PCR CD4+ x for citrulline 6 | 5 CAAGITGNTGKL TRAV4D-4 TRAJ37 CASSQFRDRGAEQ TRBV5 TRBD1 TRBJ2-1 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII GVYATXSSAVRLR VIM HomoSapiens PMID:39043656 tetramer-sort 1/32 PCR CD4+ x for citrulline 7 | 6 CALGPSGGNYKP TRAV6N-6 TRAJ6 CASSPTSSNERL TRBV2 TRBD1 TRBJ1-4 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 5/63 PCR CD4+ x for citrulline 8 | 7 CALNQGGSAKL TRAV6N-6 TRAJ57 CASSQDPSNTGQL TRBV2 TRBD1 TRBJ2-2 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 9 | 8 CALSGANTGKL TRAV6N-6 TRAJ52 CASSQDRSNTEV TRBV2 TRBD1 TRBJ1-1 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 10 | 9 CALRTGGYKV TRAV6N-6 TRAJ12 CASSQDSANTEV TRBV2 TRBD1 TRBJ1-1 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 11 | 10 CALGTGGYKV TRAV6N-6 TRAJ12 CASSRDNSNSDY TRBV2 TRBD1 TRBJ1-2 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 10/63 PCR CD4+ x for citrulline 12 | 11 CASGTGGYKV TRAV6N-6 TRAJ12 CASSLEQSNSDY TRBV3 TRBD1 TRBJ1-2 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 13 | 12 CALRNTNTGKL TRAV6N-6 TRAJ27 CASSPRHSGNTL TRBV4 TRBD1 TRBJ1-3 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 14 | 13 CALNGGSNAKL TRAV6N-6 TRAJ42 CASSPQTGGYEQ TRBV4 TRBD2 TRBJ2-7 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 15 | 14 CALTGGSNAKL TRAV6N-6 TRAJ42 CASSQGHERL TRBV4 TRBD1 TRBJ1-4 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 5/63 PCR CD4+ x for citrulline 16 | 15 CALGSGGNYKP TRAV6N-6 TRAJ6 CASSSQNSGNTL TRBV4 TRBD1 TRBJ1-3 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 3/63 PCR CD4+ x for citrulline 17 | 16 CALGTGGYKV TRAV6N-6 TRAJ12 CASSDFSVEQ TRBV13-1 TRBD1 TRBJ2-7 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 18 | 17 CAYYGSSGNKL TRAV6N-6 TRAJ32 CASSFRGDNSPL TRBV13-1 TRBD1 TRBJ1-6 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 19 | 18 CALSDGGQKL TRAV6N-6 TRAJ16 CASGDFRAEQ TRBV13-2 TRBD1 TRBJ2-1 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 20 | 19 CALGGGSALGRL TRAV6-6 TRAJ18 CASSRGGTANTGQL TRBV17 TRBD1 TRBJ2-2 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 14/63 PCR CD4+ x for citrulline 21 | 20 CALSVPNNAGAKL TRAV12N-3 TRAJ39 CASSLGQGSSYEQ TRBV26 TRBD1 TRBJ2-7 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 22 | 21 CALRGSGGNYKP TRAV6N-6 TRAJ6 CAWSLGTGQDTQ TRBV31 TRBD1 TRBJ2-5 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 1/63 PCR CD4+ x for citrulline 23 | 22 CALSGGNYKP TRAV6N-6 TRAJ6 CAWSLGQGGNERL TRBV31 TRBD1 TRBJ1-4 MusMusculus HLA-DRA*01:01 HLA-DRB1*04:01 MHCII EIFDSXGNPTVEV ENO1 HomoSapiens PMID:39043656 tetramer-sort 15/63 PCR CD4+ x for citrulline 24 | -------------------------------------------------------------------------------- /chunks/PMID_39074636.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CIVSHNAGNMLTF TRAV26-1*01 TRAJ39*01 CASSLERETQYF TRBV5-1*01 TRBD2*01 TRBJ2-5*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGPGAESCQ INS HomoSapiens PMID:39074636 antigen-expressing-targets no A2.13 8VCX 3 | 2 CIVSHNAGNMLTF TRAV26-1*01 TRAJ39*01 CASSLERETQYF TRBV5-1*01 TRBD2*01 TRBJ2-5*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGSSPETCI INS HomoSapiens PMID:39074636 antigen-expressing-targets no A2.13 8VCY 4 | 3 CIVRVAIEGSQGNLIF TRAV26-1*01 TRAJ42*01 CASSLRRGDTIYF TRBV5-1*01 TRBD1*01 TRBJ1-3*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID:39074636 antigen-expressing-targets no ET650-4 8VD0 5 | 4 CIVRVAIEGSQGNLIF TRAV26-1*01 TRAJ42*01 CASSLRRGDTIYF TRBV5-1*01 TRBD1*01 TRBJ1-3*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGTPIESCQ INS HomoSapiens PMID:39074636 antigen-expressing-targets no ET650-4 8VD2 6 | 5 CIVSHNAGNMLTF TRAV26-1*01 TRAJ39*01 CASSLERETQYF TRBV5-1*01 TRBD2*01 TRBJ2-5*01 HomoSapiens HLA-DQA1*03:01 HLA-DQB1*02:01 MHCII GQVELGGGNAVEVCK INS HomoSapiens PMID:39074636 antigen-expressing-targets no A2.13 6XCP -------------------------------------------------------------------------------- /chunks/PMID_9207000.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAVGDNFNKFYF TRAV8-3 TRAJ21 CASSRTSATGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ CA 5316 CTL A11,A32,B18,B35 3 | 2 CAVGDNFNKFYF TRAV8-3 TRAJ21 CASSLASATGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ CA 5316 CTL A11,A32,B18,B35 4 | 3 CAVGDNFNKFYF TRAV8-3 TRAJ21 CASSVTSATGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ BK 5316 CTL A2,A11,B7,B62 5 | 4 CAVGDNFNKFYF TRAV8-3 TRAJ21 CASSPTSAAGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ BK 5316 CTL A2,A11,B7,B62 6 | 5 CAVGDNFNKFYF TRAV8-3 TRAJ21 CASSLTSATGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ BK 5316 CTL A2,A11,B7,B62 7 | 6 CAVGDNFNKFYF TRAV8-3 TRAJ21 CASSLTSAAGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ BK 5316 CTL A2,A11,B7,B62 8 | 7 CAVSDITYKYIF TRAV3 TRAJ40 CATGPRANTGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ EA 5316 CTL A10,A11,B35.3,B51 9 | 8 CAVGDNFNKFYF TRAV8-3 TRAJ21 CASSRTSATGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ ZA 5316 CTL A3,A11,B35 10 | 9 CAVGDNFNKFYF TRAV8-3 TRAJ21 CASSLTSATGELFF TRBV28 TRBJ2-2 HomoSapiens HLA-A*11 B2M MHCI AVFDRKSDAK EBNA4 EBV PMID:9207000 limiting-dilution-cloning rna-seq CD8+ EBV+ ZA 5316 CTL A3,A11,B35 11 | 10 CAVSGYNAGNMLTF TRAV8-4 TRAJ39 CASSVAESPGYPPLVTEAFF TRBV9 TRBJ1-1 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 2/14 rna-seq CD8+ EBV+ BK 29466 CTL A2,A11,B7,B62 12 | 11 CAVNFAGGGADGLTF TRAV8-1 TRAJ45 CASSESAGGYYNEQFF TRBV2 TRBJ2-1 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 2/14 rna-seq CD8+ EBV+ BK 29466 CTL A2,A11,B7,B62 13 | 12 CAGHAGNQFYF TRAV35 TRAJ49 CASSFGSGSSYGYTF TRBV11-1 TRBJ1-2 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 5/14 rna-seq CD8+ EBV+ BK 29466 CTL A2,A11,B7,B62 14 | 13 CAASTNAGNNRKLIW TRAV29 TRAJ38 CSASLYGRGQPQHF TRBV20-1 TRBJ1-5 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 5/14 rna-seq CD8+ EBV+ BK 29466 CTL A2,A11,B7,B62 15 | 14 CALIQGAQKLVF TRAV16 TRAJ54 CASSLEPGRNEKLFF TRBV7-6 TRBJ1-4 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 4/4 rna-seq CD8+ EBV+ CA 29466 CTL A11,A32,B18,B35 16 | 15 CAVFYSGGSNYKLTF TRAV36 TRAJ53 CASSVGDGGANTQYF TRBV9 TRBJ2-3 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 2/6 rna-seq CD8+ EBV+ EA 29466 CTL A10,A11,B35.3,B51 17 | 16 CAGQLRNNLFF TRAV35 TRAJ36 CASTTGGATGYTF TRBV2 TRBJ1-2 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 1/6 rna-seq CD8+ EBV+ EA 29466 CTL A10,A11,B35.3,B51 18 | 17 CALMVYGGSQGNLIF TRAV12-2 TRAJ42 CASSWGGAAQFF TRBV25-1 TRBJ2-1 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 2/6 rna-seq CD8+ EBV+ EA 29466 CTL A10,A11,B35.3,B51 19 | 18 CASLSRGLLNEAFF TRBV27 TRBJ1-1 HomoSapiens HLA-A*11 B2M MHCI IVTDFSVIK EBNA4 EBV PMID:9207000 limiting-dilution-cloning 1/6 rna-seq CD8+ EBV+ EA 29466 CTL A10,A11,B35.3,B51 20 | -------------------------------------------------------------------------------- /chunks/PMID_9862375.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAVNYGNTPLVF TRAV2S1 TRAJ9S14 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 7/9 sanger antigen-loaded-targets IM53 0mo A 3 | 2 CAMREVNDYKLSF TRAV6S1 TRAJ1S3 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 2/9 sanger antigen-loaded-targets IM53 0mo B 4 | 3 CAVNYGNTPLVF TRAV2S1 TRAJ9S14 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 4/9 sanger antigen-loaded-targets IM53 16mo A 5 | 4 CILPLAGGTSYGKLTF TRAV4S1 TRAJ14S3 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 2/9 sanger antigen-loaded-targets IM53 16mo P 6 | 5 CAVLFGNEKLTF TRAV27S1 TRAJ17S8 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 2/9 sanger antigen-loaded-targets IM53 16mo C 7 | 6 CAVDTGTYKYIF TRAV13S1 TRAJ17S10 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/9 sanger antigen-loaded-targets IM53 16mo D 8 | 7 CAVNYGNTPLVF TRAV2S1 TRAJ9S14 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 4/7 sanger antigen-loaded-targets IM53 22mo A 9 | 8 CILPLAGGTSYGKLTF TRAV4S1 TRAJ14S3 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/7 sanger antigen-loaded-targets IM53 22mo P 10 | 9 CAVLFGNEKLTF TRAV27S1 TRAJ17S8 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/7 sanger antigen-loaded-targets IM53 22mo C 11 | 10 CAVSKANGSRLTF TRAV13S1 TRAJ4S1 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/7 sanger antigen-loaded-targets IM53 22mo E 12 | 11 CILPLAGGTSYGKLTF TRAV4S1 TRAJ14S3 CASSLGQAYEQYF TRBV6S3 TRBJ2S7 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 4/6 sanger antigen-loaded-targets IM63 0mo P 13 | 12 CILPLAGGTSYGKLTF TRAV4S1 TRAJ14S3 CASSSGQAYEQYF TRBV6S3 TRBJ2S7 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/6 sanger antigen-loaded-targets IM63 0mo Q 14 | 13 CILRDVFPSGSARQLTF TRAV4S1 TRAJ14S3 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/6 sanger antigen-loaded-targets IM63 0mo R 15 | 14 CILPLAGGTSYGKLTF TRAV4S1 TRAJ14S3 CASSLGQAYEQYF TRBV6S3 TRBJ2S7 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 4/7 sanger antigen-loaded-targets IM63 9mo P 16 | 15 CILRDVFPSGSARQLTF TRAV4S1 TRAJ14S3 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/7 sanger antigen-loaded-targets IM63 9mo R 17 | 16 CILRVLGSNYQLIW TRAV4S1 TRAJ1S8 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/7 sanger antigen-loaded-targets IM63 9mo S 18 | 17 CAGLGSNDYKLSF TRAV32S1 TRAJ1S3 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/7 sanger antigen-loaded-targets IM63 9mo T 19 | 18 CILPLAGGTSYGKLTF TRAV4S1 TRAJ14S3 CASSLGQAYEQYF TRBV6S3 TRBJ2S7 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 5/7 sanger antigen-loaded-targets IM63 37mo P 20 | 19 CILPLAGGTSYGKLTF TRAV4S1 TRAJ14S3 CASSSGQAYEQYF TRBV6S3 TRBJ2S7 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/7 sanger antigen-loaded-targets IM63 37mo Q 21 | 20 CILRVLGSNYQLIW TRAV4S1 TRAJ1S8 HomoSapiens HLA-B*08:01 B2M MHCI FLRGRAYGL EBNA3A EBV PMID:9862375 antigen-loaded-targets 1/7 sanger antigen-loaded-targets IM63 37mo S 22 | -------------------------------------------------------------------------------- /chunks/PMID_9971792.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CASKVGAGGLYEQYF TRBV14-1 TRBJ1-1 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 3 | 2 CASMGNSAGANVLTF TRBV17-1 TRBJ2-6 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 4 | 3 CASRGQGFSYEQYF TRBV13-1 TRBJ2-7 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 5 | 4 CASSFLGLNEQFF TRBV6 TRBJ2-1 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 6 | 5 CASSFRDYGNYEQYF TRBV6-4 TRBJ2-1 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 7 | 6 CASSIGPALNTEAFF TRBV14-1 TRBJ1-1 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 8 | 7 CASSLDIPSYNEQFF TRBV6 TRBJ2-1 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 9 | 8 CILRGGGADGLTF TRAV4-1 TRAJ45 CASSLGGNLYEQYF TRBV6-4 TRBJ2-7 HomoSapiens HLA-B*12 B2M MHCI EFFWDANDIY pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 10 | 9 CAMREGMDSSYKLIF TRAV6-1 TRAJ31 CASSLHDRGSRTEAFF TRBV6-4 TRBJ1-1 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 11 | 10 CATVLRMDSSYKLIF TRAV3-1 TRAJ31 CASSLIGVSSYNEQFF TRBV6-4 TRBJ2-1 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 12 | 11 CASSPARNTEAFF TRBV7-2 TRBJ1-1 HomoSapiens HLA-B*07 B2M MHCI RPHERNGFTV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 13 | 12 CASSPHRNTEAFF TRBV7-2 TRBJ1-1 HomoSapiens HLA-B*07 B2M MHCI RPHERNGFTV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 14 | 13 CASSPSRNTEAFF TRBV7-2 TRBJ1-1 HomoSapiens HLA-B*07 B2M MHCI RPHERNGFTV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 15 | 14 CASSQAALAGFGYEQYF TRBV7-1 TRBJ2-7 HomoSapiens HLA-B*07 B2M MHCI RPHERNGFTV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 16 | 15 CAEIHNNARLMF TRAV8-2 TRAJ12 CASSSANYGYTF TRBV8 TRBJ1-2 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 17 | 16 CASSSHDRQGASSPLHF TRBV6-4 TRBJ1-6 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 18 | 17 CASSSHDTGGYNSPLHF TRBV6-4 TRBJ1-6 HomoSapiens HLA-B*07 B2M MHCI TPRVTGGGAM pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 19 | 18 CASSSVNEQFF TRBV8 TRBJ2-1 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 20 | 19 CASSSVSEAFF TRBV8 TRBJ1-1 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 21 | 20 CASSYQTGTGNYGYTF TRBV13-1 TRBJ1-2 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 22 | 21 CASSYSGHVYEQYF TRBV13-1 TRBJ2-7 HomoSapiens HLA-A*02 B2M MHCI NLVPMVATV pp65 CMV PMID:9971792 limited-dilution-cloning,antigen-expressing-targets 1 antigen-expressing-targets 23 | -------------------------------------------------------------------------------- /chunks/paley-etal-2024-06-18.txt: -------------------------------------------------------------------------------- 1 | chunk.id cdr3.alpha v.alpha j.alpha cdr3.beta v.beta d.beta j.beta species mhc.a mhc.b mhc.class antigen.epitope antigen.gene antigen.species reference.id method.identification method.frequency method.singlecell method.sequencing method.verification meta.study.id meta.cell.subset meta.subset.frequency meta.subject.cohort meta.subject.id meta.replica.id meta.clone.id meta.epitope.id meta.tissue meta.donor.MHC meta.donor.MHC.method meta.structure.id 2 | 1 CAFGGTSYGKLTF TRAV29/DV5 CSARPWETTEAFF TRBV20-1 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ Healthy PBMC 3 | 2 CAVDSPGTYKYIF TRAV39 CASSLGKFGNQPQHF TRBV7-9 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 4 | 3 CGIALIGSGAGSYQLTF TRAV21 CASSPATYSTDTQYF TRBV9 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 5 | 4 CAVLSNAGGTSYGKLTF TRAV21 CASNLGTSGPGDTQYF TRBV6-2 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 6 | 5 CAVGPPSNFGNEKLTF TRAV8-3 CASSPDSLNEKLFF TRBV5-5 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 7 | 6 CAVSANYGGSQGNLIF TRAV21 CASSLAYYSTDTQYF TRBV9 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 8 | 7 CAVDSFNTQGAQKLVF TRAV21 CASSPWGTYSTDTQYF TRBV9 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 9 | 8 CAALSQGGSEKLVF TRAV21 CASSVAYYSTDTQYF TRBV9 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 10 | 9 CAFMKLMYSGGGADGLTF TRAV38-1 CASSLEGGDSYGYTF TRBV13 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU-alone PBMC 11 | 10 CAVLGFQKLVF TRAV21 CASSLEVYSTDTQYF TRBV5-1 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 12 | 11 CAVGGFGGGSNYKLTF TRAV21 CASSSSYSTDTQYF TRBV7-6 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 13 | 12 CAVRGFNQAGTALIF TRAV21 CASSLATYSTDTQYF TRBV5-5 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 14 | 13 CAVNSPSYSGAGSYQLTF TRAV21 CASSPGTFSTDTQYF TRBV9 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 15 | 14 CAVRSNQAGTALIF TRAV21 CASSFGLYSTDTQYF TRBV5-4 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 16 | 15 CAYRSPNAGNNRKLIW TRAV38-2/DV8 CASSLGRYSSYEQYF TRBV5-5 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 17 | 16 CAAPYGGSQGNLIF TRAV21 CASSVAYYSTDTQYF TRBV9 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 18 | 17 CAASSGYALNF TRAV21 CASSDGYSTDTQYF TRBV5-1 HLA-B*27 B2M MHCI LRVMMLAPF yeiH E.Coli doi:10.1172/jci.insight.174776 tetramer-sort yes amplicon-seq CD8+ B27AAU/r-axSpA PBMC 19 | -------------------------------------------------------------------------------- /database/dummy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/antigenomics/vdjdb-db/4fe22b7969d0ab8c6910bbdce51c06f1f33679ea/database/dummy -------------------------------------------------------------------------------- /images/vdjdb-splash.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/antigenomics/vdjdb-db/4fe22b7969d0ab8c6910bbdce51c06f1f33679ea/images/vdjdb-splash.png -------------------------------------------------------------------------------- /latest-version.txt: -------------------------------------------------------------------------------- 1 | https://github.com/antigenomics/vdjdb-db/releases/download/pyvdjdb-2025-02-21/vdjdb-2025-02-21.zip 2 | https://github.com/antigenomics/vdjdb-db/releases/download/pyvdjdb-2024-11-27/vdjdb-2024-11-27-fixed.zip 3 | https://github.com/antigenomics/vdjdb-db/releases/download/2024-06-13/vdjdb-2024-06-13.zip 4 | https://github.com/antigenomics/vdjdb-db/releases/download/2024-05-23/vdjdb-2024-05-23.zip 5 | https://github.com/antigenomics/vdjdb-db/releases/download/2023-06-01/vdjdb-2023-06-01.zip 6 | https://github.com/antigenomics/vdjdb-db/releases/download/2022-03-30/vdjdb-2022-03-30.zip 7 | https://github.com/antigenomics/vdjdb-db/releases/download/2022-03-13/vdjdb-2022-03-13.zip 8 | https://github.com/antigenomics/vdjdb-db/releases/download/2022-03-10/vdjdb-2022-03-10.zip 9 | https://github.com/antigenomics/vdjdb-db/releases/download/2022-02-23/vdjdb-2022-02-23.zip 10 | https://github.com/antigenomics/vdjdb-db/releases/download/2022-02-22/vdjdb-2022-02-22.zip 11 | https://github.com/antigenomics/vdjdb-db/releases/download/2021-09-05/vdjdb-2021-09-05.zip 12 | https://github.com/antigenomics/vdjdb-db/releases/download/2021-02-02/vdjdb-2021-02-02.zip 13 | https://github.com/antigenomics/vdjdb-db/releases/download/2021-01-10/vdjdb-2021-01-10.zip 14 | https://github.com/antigenomics/vdjdb-db/releases/download/2020-05-20/vdjdb-2020-05-20.zip 15 | https://github.com/antigenomics/vdjdb-db/releases/download/2020-01-20/vdjdb-2020-01-20.zip 16 | https://github.com/antigenomics/vdjdb-db/releases/download/2019-08-08/vdjdb-2019-08-08.zip 17 | https://github.com/antigenomics/vdjdb-db/releases/download/2018-06-04/vdjdb-2018-06-04.zip 18 | https://github.com/antigenomics/vdjdb-db/releases/download/2018-05-05/vdjdb-2018-05-05.zip 19 | https://github.com/antigenomics/vdjdb-db/releases/download/2018-01-17/vdjdb-2018-01-17.zip 20 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-11-26/vdjdb-2017-11-26.zip 21 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-10-27/vdjdb-2017-10-27.zip 22 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-09-04/vdjdb-2017-09-04.zip 23 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-08-03/vdjdb-2017-08-03.zip 24 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-06-13/vdjdb-2017-06-13.zip 25 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-05-25/vdjdb-2017-05-25.zip 26 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-03-18/vdjdb-2017-03-18.zip 27 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-03-10/vdjdb-2017-03-10.zip 28 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-02-02/vdjdb-2017-02-02.zip 29 | https://github.com/antigenomics/vdjdb-db/releases/download/2017-01-08/vdjdb-2017-01-08.zip 30 | https://github.com/antigenomics/vdjdb-db/releases/download/2016-09-05/vdjdb-2016-09-05.zip 31 | https://github.com/antigenomics/vdjdb-db/releases/download/2016-07-08/vdjdb-2016-07-08.zip 32 | https://github.com/antigenomics/vdjdb-db/releases/download/2016-06-25/vdjdb-2016-06-25.zip 33 | https://github.com/antigenomics/vdjdb-db/releases/download/2016-06-15/vdjdb-2016-06-15.zip 34 | https://github.com/antigenomics/vdjdb-db/releases/download/2016-05-31/vdjdb-2016-05-31.zip 35 | https://github.com/antigenomics/vdjdb-db/releases/download/2016-05-05/vdjdb-2016-05-05.zip 36 | https://github.com/antigenomics/vdjdb-db/releases/download/2016-05-02/vdjdb-2016-05-02.zip 37 | -------------------------------------------------------------------------------- /patches/antigen_epitope_species_gene.dict: -------------------------------------------------------------------------------- 1 | antigen.epitope antigen.species antigen.gene 2 | KLGGALQAK CMV IE1 3 | AYAQKIFKI CMV IE1 4 | VTEHDTLLY CMV IE1 5 | ELRRKMMYM CMV IE1 6 | YILEETSVM CMV IE1 7 | ELKRKMIYM CMV IE1 8 | CVETMCNEY CMV IE1 9 | DEEDAIAAY CMV IE1 10 | VLEETSVML CMV IE1 11 | LSEFCRVLCCYVLEE CMV IE1 12 | QIKVRVDMV CMV IE1 13 | QIKVRVKMV CMV IE1 14 | NEGVKAAW CMV IE2 15 | VTEHDTLLY CMV pp50 16 | IPSINVHHY CMV pp65 17 | QYDPVAALF CMV pp65 18 | TPRVTGGGAM CMV pp65 19 | RPHERNGFTVL CMV pp65 20 | NLVPMVATV CMV pp65 21 | CPSQEPMSIYVY CMV pp65 22 | FPTKDVAL CMV pp65 23 | EDVPSGKLFMHVTLG CMV pp65 24 | ARNLVPMVATVQGQN CMV pp65 25 | YSEHPTFTSQY CMV pp65 26 | MLNIPSINV CMV pp65 27 | EFFWDANDIY CMV pp65 28 | RPHERNGFTV CMV pp65 29 | VMAPRTLIL CMV UL40 30 | GTSGSPIVNR DENV NS3 31 | GTSGSPIIDK DENV NS3 32 | GTSGSPIINR DENV NS3 33 | GLCTLVAML EBV BMLF1 34 | YVLDHLIVV EBV BRLF1 35 | RAKFKQLL EBV BZLF1 36 | LPEPLPQGQLTAY EBV BZLF1 37 | EPLPQGQLTAY EBV BZLF1 38 | GPEPLPQGQLTAY EBV BZLF1 39 | LPEGLPQGQLTAY EBV BZLF1 40 | LPEPLGQGQLTAY EBV BZLF1 41 | LPEPLPQAQLTAY EBV BZLF1 42 | LPEPLPQGGLTAY EBV BZLF1 43 | LPEPLPQGQGTAY EBV BZLF1 44 | LPEPLPQGQLGAY EBV BZLF1 45 | LPEPLPQGQLTGY EBV BZLF1 46 | HPVGEADYFEY EBV EBNA1 47 | HPVGDADYFEY EBV EBNA1 48 | HPVGQADYFEY EBV EBNA1 49 | RLRAEAQVK EBV EBNA3A 50 | FLRGRAYGL EBV EBNA3A 51 | RPPIFIRRL EBV EBNA3A 52 | EENLLDFVRF EBV EBNA3A 53 | YPLHEQHGM EBV EBNA3A 54 | IVTDFSVIK EBV EBNA3B 55 | AVFDRKSDAK EBV EBNA3B 56 | LLDFVRFMGV EBV EBNA3B 57 | VSFIEFVGW EBV EBNA3B 58 | IVTDFSVIK EBV EBNA4 59 | QPRAPIRPI EBV EBNA6 60 | EENLLDFVRF EBV EBNA6 61 | YLLEMLWRL EBV LMP1 62 | FLYALALLL EBV LMP2A 63 | CLGGLLTMV EBV LMP2A 64 | GAMKRHGLDNYRGYSLG GallusGallus LYZ 65 | SIINFEKL GallusGallus OVA 66 | GNSHRGAIEWEGIESG GallusGallus Ovotransferrin 67 | HSKKKCDEL HCV NS3 68 | ATDALMTGY HCV NS3 69 | CINGVCWTV HCV NS3 70 | KLVALGINAV HCV NS3 71 | KLSALGINAV HCV NS3 72 | ARMILMTHF HCV NS5B 73 | SLFNTVATLY HIV-1 Gag 74 | RTLNAWVKV HIV-1 Gag 75 | SLFNTVATL HIV-1 Gag 76 | SLYNTVATLY HIV-1 Gag 77 | KAFSPEVIPMF HIV-1 Gag 78 | KRWIILGLNK HIV-1 Gag 79 | KRWIIMGLNK HIV-1 Gag 80 | TAFTIPSI HIV-1 Gag 81 | TPQDLNTML HIV-1 Gag 82 | EIYKRWII HIV-1 Gag 83 | RLRPGGKKK HIV-1 Gag 84 | GPGMKARVL HIV-1 Gag 85 | SLYNTVATL HIV-1 Gag 86 | CTPYDINQM HIV-1 Gag 87 | TLNAWVKVV HIV-1 Gag 88 | KINAWIKVV HIV-1 Gag 89 | GPGHKARVL HIV-1 Gag 90 | GLNKIVRMY HIV-1 Gag 91 | QASQEVKNW HIV-1 Gag 92 | FLGKIWPSHK HIV-1 Gag 93 | RLRPGGKKR HIV-1 Gag 94 | RLRPGGRKR HIV-1 Gag 95 | GEIYKRWII HIV-1 Gag 96 | ISPRTLNAW HIV-1 Gag 97 | FRDYVDRFYKTLRAEQASQE HIV-1 Gag 98 | DRFYKTLRAEQASQEV HIV-1 Gag 99 | LNKIVRMYSPTSILD HIV-1 Gag 100 | RFPLTFGWCF HIV-1 Nef 101 | RYPLTFGWCF HIV-1 Nef 102 | RYPLTLGWCF HIV-1 Nef 103 | FLKEKGGL HIV-1 Nef 104 | FLKEQGGL HIV-1 Nef 105 | FLKETGGL HIV-1 Nef 106 | FLKEMGGL HIV-1 Nef 107 | QVPLRPMTYK HIV-1 Nef 108 | TQGYFPDWQNY HIV-1 Nef 109 | TPGPGVRYPL HIV-1 Nef 110 | ILKEPVHGV HIV-1 Pol 111 | ISPRTLNAW HIV-1 Pol 112 | FPQGEAREL HIV-1 Pol 113 | TAFTIPSI HIV-1 Pol 114 | IIKDYGKQM HIV-1 Pol 115 | LPPIVAKEI HIV-1 Pol 116 | HPKVSSEVHI HIV-1 Vif 117 | FPRPWLHGL HIV-1 Vpr 118 | EEYLQAFTY HomoSapiens ABCD3 119 | KLMNIQQKL HomoSapiens AKAP13 120 | RIAAWMATY HomoSapiens BCL2L1 121 | YLNDHLEPWI HomoSapiens BCL2L1 122 | LLLGIGILV HomoSapiens BST2 123 | LGYGFVNYI HomoSapiens ELAVL4 124 | KIFGSLAFL HomoSapiens ERBB2 125 | IILVAVPHV HomoSapiens EXOC8 126 | NLSALGIFST HomoSapiens IGF2BP2 127 | ALWGPDPAAA HomoSapiens INS 128 | QPLALEGSLQKRG HomoSapiens INS 129 | LQPLALEGSLQKRG HomoSapiens INS 130 | KLQCVDLHV HomoSapiens KLK3 131 | KVLEYVIKV HomoSapiens MAGEA1 132 | KVAELVHFL HomoSapiens MAGEA3 133 | VHFFKNIVTPRTPG HomoSapiens MBP 134 | PADPLAFFSSAIKGGGGSLV HomoSapiens MCC 135 | ADGLAYFRSSFKGG HomoSapiens MCC 136 | ANGVAFFLTPFKA HomoSapiens MCC 137 | ELAGIGILTV HomoSapiens MLANA 138 | EEYLKAWTF HomoSapiens MLANA 139 | AAGIGILTV HomoSapiens MLANA 140 | ALGIGILTV HomoSapiens MLANA 141 | ELAAIGILTV HomoSapiens MLANA 142 | ELAGIGALTV HomoSapiens MLANA 143 | EAAGIGILTV HomoSapiens MLANA 144 | ELAGIGLTV HomoSapiens MLANA 145 | EEAAGIGIL HomoSapiens MLANA 146 | CLNEYHLFL HomoSapiens NDC1 147 | SLLMWITQV HomoSapiens NY-ESO-1 148 | SLLMWITQC HomoSapiens NY-ESO-1 149 | MLGEQLFPL HomoSapiens PABPC1 150 | FLASKIGRLV HomoSapiens PLA2G6 151 | IMDQVPFSV HomoSapiens PMEL 152 | KTWGQYWQV HomoSapiens PMEL 153 | FLYNLLTRV HomoSapiens SEC24A 154 | VAANIVLTV HomoSapiens SLC30A8 155 | ILAKFLHWL HomoSapiens TERT 156 | AMFWSVPTV HomoSapiens TKT 157 | GELIGILNAAKVPAD HomoSapiens TPI1 158 | GELIGTLNAAKVPAD HomoSapiens TPI1 159 | CLLWSFQTSA HomoSapiens TYR 160 | CYTWNQMNL HomoSapiens WT1 161 | RMFPNAPYL HomoSapiens WT1 162 | MLDLQPETT HPV E7 163 | RPRGEVRFL HSV-2 UL49 164 | LLFGYPVYV HTLV-1 Tax 165 | LLFGYAVYV HTLV-1 Tax 166 | LLFGYPRYV HTLV-1 Tax 167 | LLFGYPVAV HTLV-1 Tax 168 | LLFGKPVYV HTLV-1 Tax 169 | LLFGPVYV HTLV-1 Tax 170 | LLFGFPVYV HTLV-1 Tax 171 | SFHSLHLLF HTLV-1 Tax 172 | PKYVKQNTLKLAT InfluenzaA HA 173 | PKYVKQNTLKLRT InfluenzaA HA 174 | PKYVKQNTLKLAR InfluenzaA HA 175 | GILGFVFTL InfluenzaA M 176 | CTELKLSDY InfluenzaA NP 177 | LPRRSGAAGA InfluenzaA NP 178 | ASNENMETM InfluenzaA NP 179 | SSLENFRAYV InfluenzaA PA 180 | LSLRNPILV InfluenzaA PB1 181 | SSYRRPVGI InfluenzaA PB1 182 | CVNGSCFTV InfluenzaA NA 183 | KAVYNFATC LCMV GPC 184 | ADLIAYLKQATKG ManducaSexta MCC 185 | TVYGFCLL MCMV m139 186 | SSPPMFRV MCMV M38 187 | HGIRNASFI MCMV M45 188 | KVITFIDL MusMusculus Gtpbp1 189 | INFDFNTI MusMusculus Kctd20 190 | SRGGASQYRPSQ MusMusculus Mbp 191 | RGGASQYRPSQ MusMusculus Mbp 192 | EQYKFYSV MusMusculus Ndufa4 193 | SQYYYNSL MusMusculus Rbm5 194 | SQLLNAKYL PlasmodiumBerghei GAP50 195 | NAITNAKII RSV M 196 | SYIGSINNI RSV M2-1 197 | MLWGYLQYV SaccharomycesCerevisiae Tel1 198 | CTPYDINQM SIV Gag 199 | TTPESANL SIV Tat 200 | STPESANL SIV Tat 201 | CLLGTYTQDV StreptomycesKanamyceticus KanJ 202 | SIYRYYGL Synthetic Synthetic 203 | WIYVYRPMGCGGS Synthetic Synthetic 204 | SGEGSFQPSQENP TriticumAestivum Gliadin 205 | APQPELPYPQPGS TriticumAestivum Gliadin 206 | APQPELPYPQPG TriticumAestivum Gliadin 207 | QPFPQPELPYP TriticumAestivum Gliadin 208 | PSGEGSFQPSQENPQ TriticumAestivum Gliadin 209 | QLQPFPQPELPY TriticumAestivum Gliadin 210 | PQPELPYPQPQL TriticumAestivum Gliadin 211 | FPQPEQPFPWQP TriticumAestivum Gliadin 212 | PFPQPELPY TriticumAestivum Gliadin 213 | PQPELPYPQ TriticumAestivum Gliadin 214 | PQPELPYPQPE TriticumAestivum Gliadin 215 | PQPELPYPQPQ TriticumAestivum Gliadin 216 | PQPQLPYPQPQ TriticumAestivum Gliadin 217 | PQQPFPQPEQPFP TriticumAestivum Gliadin 218 | LQPFPQPELPYGSGGS TriticumAestivum Gliadin 219 | QPFPQPEQPFP TriticumAestivum Gliadin 220 | RGYVYQGL VSV N 221 | RGYVYKGL VSV N 222 | RGYVYEGL VSV N 223 | RGYVYDGL VSV N 224 | IGYVYQGL VSV N 225 | KGYVYQGL VSV N 226 | LLWNGPMAV YFV NS4B 227 | RPGGKKHYM HIV-1 Nef 228 | RMYSPVSI HIV-1 Gag 229 | RMYSPVSIL HIV-1 Gag 230 | ALHGGWTTK HomoSapiens PIK3CA 231 | HMTEVVRHC HomoSapiens p53 232 | HMTEVVRHC HomoSapiens p53 233 | PGVLLKEFTVSGNIL HomoSapiens NY-ESO-1 234 | APRGPHGGAASGL HomoSapiens NY-ESO-1 235 | TSTLQEQIGW HIV-1 Gag 236 | HTQGYFPD HIV-1 Nef 237 | RPGGKKHYM HIV-1 Nef 238 | KRKGGIGGY HIV-1 Pol 239 | IPLTEEAEL HIV-1 Pol 240 | IVLPEDKSW HIV-1 RT 241 | GADGVGKSAL HomoSapiens KRAS 242 | ALTPVVVTL HomoSapiens UNC-CDK4-1 243 | VEELYLVAGEEGCGGGGSL HomoSapiens Insulin 244 | TTDPSFLGRY SARS-CoV-2 ORF1ab 245 | YLEPGPVTV HomoSapiens PMEL -------------------------------------------------------------------------------- /patches/nomenclature.conversions: -------------------------------------------------------------------------------- 1 | #primer sequences may help https://droog.gs.washington.edu/tcr/tcr_home.html; for BV only 2 | TRAV23S1 TRAV27 3 | TRAV15S1 TRAV5,TRAV13-2 4 | TRAV2S3 TRAV12-1 5 | TRAV21S1 TRAV13-1,TRAV23/DV6,TRAV29/DV5 6 | TRAV4S1 TRAV26-2 7 | TRAV5S1 TRAV6 8 | TRAV3S2 TRAV12-1 9 | TRAV3S1 TRAV17 10 | TRAV1S2 TRAV8-6,TRAV8-4 11 | TRAV14S2 TRAV38-1 12 | TRAV10S2 TRAV27 13 | TRAV8S1 TRAV13-1,TRAV23/DV6,TRAV29/DV5 14 | TRAV2S2 TRAV9-2 15 | TRAJ14S1 TRAJ37 16 | TRAJ14S2 TRAJ23 17 | TRAJ14S3 TRAJ52 18 | TRAJ15S1 TRAJ16 19 | TRAJ16S1 TRAJ3 20 | TRAJ16S5 TRAJ12 21 | TRAJ16S6 TRAJ5 22 | TRAJ17S1 TRAJ34 23 | TRAJ17S10 TRAJ40 24 | TRAJ17S5 TRAJ36 25 | TRAJ1S3 TRAJ20 26 | TRAJ1S7 TRAJ43 27 | TRAJ3S2 TRAJ31 28 | TRAJ8S1 TRAJ13 29 | TRAJ9S11 TRAJ42 30 | TRAJ9S12 TRAJ56 31 | TRAJ9S14 TRAJ29 32 | TRAJ9S15 TRAJ11 33 | TRAJ14S1 TRAJ37 34 | TRAJ9S11 TRAJ42 35 | TRAJ9S4 TRAJ30 36 | TRBV1S1 TRBV9 37 | TRBV13S1 TRBV6-5 38 | TRBV13S2 TRBV6-2,TRBV6-3 39 | TRBV13S3 TRBV6-1 40 | TRBV13S4 TRBV6-9 41 | TRBV16S1 TRBV14 42 | TRBV17S1 TRBV19 43 | TRBV21S3 TRBV11-2 44 | TRBV22S1 TRBV2 45 | TRBV2S1 TRBV20-1 46 | TRBV4S1 TRBV29-1 47 | TRBV6S7 TRBV7-1 48 | TRBV7S1 TRBV4-1 49 | TRBJ1S1 TRBJ1-1 50 | TRBJ1S2 TRBJ1-2 51 | TRBJ1S3 TRBJ1-3 52 | TRBJ1S4 TRBJ1-4 53 | TRBJ1S5 TRBJ1-5 54 | TRBJ2S10 TRBJ2-4 55 | TRBJ2S11 TRBJ2-5 56 | TRBJ2S13 TRBJ2-7 57 | TRBJ2S7 TRBJ2-1 58 | TRBJ2S8 TRBJ2-2 59 | TRBJ2S9 TRBJ2-3 60 | TRBV6S4 TRBV7-9 -------------------------------------------------------------------------------- /release.sh: -------------------------------------------------------------------------------- 1 | # Compile database 2 | 3 | cd src/ 4 | groovy -cp . BuildDatabase.groovy 5 | cd .. 6 | 7 | # Summary HTML 8 | 9 | cd summary/ 10 | Rscript -e "rmarkdown::render('vdjdb_summary.Rmd')" 11 | groovy MakeEmbedableHtml.groovy 12 | cd .. 13 | 14 | 15 | # Compute motifs 16 | if [ -d "../vdjdb-motifs" ] 17 | then 18 | echo "Found 'vdjdb-motifs' folder. Processing..." 19 | 20 | mkdir ../vdjdb-motifs/vdjdb_dump/ 21 | cp -r database/*.txt ../vdjdb-motifs/vdjdb_dump/ 22 | 23 | cd ../vdjdb-motifs/ 24 | Rscript -e "rmarkdown::render('compute_vdjdb_motifs.Rmd')" 25 | cp cluster_members.txt ../vdjdb-db/database/ 26 | cp motif_pwms.txt ../vdjdb-db/database/ 27 | cd ../vdjdb-db/ 28 | else 29 | echo "'vdjdb-motifs' folder is missing. Skipping..." 30 | fi 31 | 32 | # Gather database 33 | 34 | cd database/ 35 | DD=`date +%F` 36 | mkdir vdjdb-$DD 37 | cp ../summary/vdjdb_summary_embed.html vdjdb-$DD/ 38 | cp *.txt vdjdb-$DD/ 39 | 40 | # Update latest version 41 | 42 | RR="https://github.com/antigenomics/vdjdb-db/releases/download/$DD/vdjdb-$DD.zip" 43 | RRP=`cat ../latest-version.txt | head -n 1` 44 | 45 | if [[ $RRP != $RR ]]; 46 | then 47 | echo "Releasing" 48 | echo $RR | cat - ../latest-version.txt > temp && mv temp ../latest-version.txt 49 | else 50 | echo "Overwriting" 51 | fi 52 | 53 | cp ../LICENSE.txt vdjdb-$DD/ 54 | cp ../latest-version.txt vdjdb-$DD/ 55 | 56 | # ZIP together 57 | 58 | zip -rj vdjdb-$DD.zip vdjdb-$DD/ 59 | 60 | echo "scp `hostname`:`pwd`/vdjdb-$DD.zip ." -------------------------------------------------------------------------------- /release_docker.sh: -------------------------------------------------------------------------------- 1 | docker build --no-cache -t vdjdbdb . 2>&1 | tee database/docker_build.log 2 | docker run -v `pwd`/database:/root/output vdjdbdb 2>&1 | tee database/docker_run.log -------------------------------------------------------------------------------- /src/Cdr3Fixer.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | class Cdr3Fixer { 18 | final Map> segmentsBySequencePartBySpeciesGene = new HashMap<>() 19 | final Map> segmentsByIdBySpecies = new HashMap<>() 20 | final int maxReplaceSize, minHitSize 21 | 22 | static Map nomenclatureConversions = new File("../patches/nomenclature.conversions") 23 | .readLines() 24 | .findAll { !it.startsWith("#") } 25 | .collectEntries { def splitLine = it.split("[\t ]+"); [(splitLine[0]): splitLine[1].split(",")[0]] } 26 | 27 | Cdr3Fixer(String segmentsFileName, String segmentsSeqFileName, 28 | int maxReplaceSize = 1, int minHitSize = 2) { 29 | this.maxReplaceSize = maxReplaceSize 30 | this.minHitSize = minHitSize 31 | 32 | new File(segmentsFileName).splitEachLine('\t') { splitLine -> 33 | if (!splitLine[0].startsWith("#")) { 34 | def species = splitLine[0].toLowerCase(), 35 | type = splitLine[2].toLowerCase(), id = splitLine[3], 36 | refPoint = splitLine[4].toInteger(), seq = splitLine[5] 37 | 38 | def segmentsById = segmentsByIdBySpecies[species] 39 | 40 | if (segmentsById == null) 41 | segmentsByIdBySpecies.put(species, segmentsById = new HashMap()) 42 | 43 | if (type.startsWith("v") || type.startsWith("j")) { 44 | boolean isJSegment = type.startsWith("j") 45 | seq = isJSegment ? seq.substring(0, refPoint + 4) : seq.substring(refPoint - 3) 46 | 47 | segmentsById.put(id, Util.translateLinear(seq, isJSegment)) 48 | } 49 | } 50 | } 51 | 52 | boolean firstLine = true 53 | new File(segmentsSeqFileName).splitEachLine('\t') { splitLine -> 54 | if (firstLine) { 55 | firstLine = false 56 | } else { 57 | def speciesChain = splitLine[0] + "." + 58 | (splitLine[1] == "TRA" ? "alpha" : "beta") // see invokation in BuildDatabase 59 | 60 | def segmentSeqMap = segmentsBySequencePartBySpeciesGene[speciesChain] 61 | 62 | if (segmentSeqMap == null) { 63 | segmentsBySequencePartBySpeciesGene.put(speciesChain, segmentSeqMap = new HashMap()) 64 | } 65 | 66 | segmentSeqMap.put(splitLine[2], splitLine[4]) // segment id by part 67 | } 68 | } 69 | } 70 | 71 | String getClosestId(String species, String id) { 72 | def segmentsById = segmentsByIdBySpecies[species.toLowerCase()] 73 | 74 | if (species.toLowerCase() == "homosapiens") { 75 | def conversion = nomenclatureConversions[id] 76 | if (conversion) { 77 | id = conversion 78 | } 79 | } 80 | 81 | if (segmentsById == null) 82 | return null 83 | 84 | // Doing an extensive search 85 | // with all possible combinations 86 | 87 | [id, Util.simplifySegmentName(id)].flatten().collect { String it -> 88 | [it, 89 | "$it*01".toString(), 90 | it.contains("-") ? [] : (1..100).collect { int i -> "$it-$i*01".toString() }] 91 | }.flatten().find { 92 | segmentsById.containsKey(it) 93 | } 94 | } 95 | 96 | String getSegmentSeq(String species, String id) { 97 | if (id == null) 98 | return null 99 | 100 | def segmentsById = segmentsByIdBySpecies[species.toLowerCase()] 101 | 102 | if (segmentsById == null) 103 | return null 104 | 105 | segmentsById[id] 106 | } 107 | 108 | OneSideFixerResult fix(String cdr3, String id, String species, boolean fivePrime) { 109 | String closestId = getClosestId(species, id) 110 | String segmentSeq = getSegmentSeq(species, closestId) 111 | 112 | if (!segmentSeq) { 113 | return new OneSideFixerResult(fivePrime ? cdr3 : cdr3.reverse(), closestId, FixType.FailedBadSegment) 114 | } 115 | 116 | if (!fivePrime) { 117 | cdr3 = cdr3.reverse() 118 | segmentSeq = segmentSeq.reverse() 119 | } 120 | 121 | def scanner = new KmerScanner(segmentSeq, minHitSize) 122 | 123 | def hit = scanner.scan(cdr3) 124 | 125 | if (hit) { 126 | if (hit.startInSegment == 0) { 127 | if (hit.startInCdr3 == 0) { 128 | return new OneSideFixerResult(cdr3, closestId, FixType.NoFixNeeded, hit.matchSize) 129 | } else { 130 | return new OneSideFixerResult(cdr3.substring(hit.startInCdr3), closestId, FixType.FixTrim, hit.matchSize) 131 | } 132 | } else { 133 | if (hit.startInCdr3 == 0) { 134 | return new OneSideFixerResult(segmentSeq.substring(0, hit.startInSegment) + cdr3, closestId, FixType.FixAdd, hit.matchSize) 135 | } else if (hit.startInCdr3 <= maxReplaceSize) { 136 | return new OneSideFixerResult(segmentSeq.substring(0, hit.startInSegment) + cdr3.substring(hit.startInCdr3), closestId, FixType.FixReplace, hit.matchSize) 137 | } else { 138 | return new OneSideFixerResult(cdr3, closestId, FixType.FailedReplace) 139 | } 140 | } 141 | } else { 142 | return new OneSideFixerResult(cdr3, closestId, FixType.FailedNoAlignment) 143 | } 144 | } 145 | 146 | String guessId(String cdr3, String species, String gene, boolean fivePrime) { 147 | def segmentSeqMap = segmentsBySequencePartBySpeciesGene[(String) (species + "." + gene)] 148 | 149 | if (segmentSeqMap == null) { 150 | return "" 151 | } 152 | 153 | if (fivePrime) { 154 | for (int i = cdr3.length() - 4; i > 1; i--) { 155 | def res = segmentSeqMap[cdr3.substring(0, i)] 156 | if (res != null) 157 | return res 158 | } 159 | return "" 160 | } else { 161 | for (int i = 2; i < cdr3.length() - 3; i++) { 162 | def res = segmentSeqMap[cdr3.substring(i)] 163 | if (res != null) 164 | return res 165 | } 166 | return "" 167 | } 168 | } 169 | 170 | FixerResult fix(String cdr3, String vId, String jId, String species, String gene) { 171 | def vResult = vId.split(",").collect { 172 | fix(cdr3, it, species, true) 173 | }.min { it.fixType.rank } 174 | 175 | def jResult = jId.split(",").collect { 176 | fix(vResult.cdr3, it, species, false) 177 | }.min { it.fixType.rank } 178 | 179 | def newCdr3 = jResult.cdr3.reverse() 180 | 181 | // 182 | // ---- 4 183 | // ---- 4 184 | // 0123456789 185 | // CASSLPKLFF 186 | // 187 | // 10 - 4 = 6 188 | 189 | new FixerResult(newCdr3, cdr3, newCdr3 != cdr3, 190 | vResult.x, 191 | jResult.x < 0 ? jResult.x : newCdr3.length() - jResult.x, 192 | vResult.segmentId, vResult.fixType, 193 | jResult.segmentId, jResult.fixType) 194 | } 195 | } -------------------------------------------------------------------------------- /src/FixType.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | 18 | enum FixType { 19 | NoFixNeeded(false, true, 0), 20 | FixAdd(true, true, 2), FixTrim(true, true, 1), 21 | FixReplace(true, true, 3), FailedReplace(true, false, 5), 22 | FailedBadSegment(false, false, 4), 23 | FailedNoAlignment(true, false, 6) 24 | 25 | final boolean fixAttempted, good 26 | final int rank 27 | 28 | FixType(boolean fixAttempted, boolean good, int rank) { 29 | this.fixAttempted = fixAttempted 30 | this.good = good 31 | this.rank = rank 32 | } 33 | } -------------------------------------------------------------------------------- /src/FixerResult.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | class FixerResult { 18 | final String cdr3, cdr3_old, vId, jId 19 | final int vEnd, jStart 20 | final boolean vCanonical, jCanonical, fixNeeded 21 | final FixType vFixType, jFixType 22 | 23 | FixerResult(String cdr3, String cdr3_old, boolean fixNeeded, int vEnd, int jStart, 24 | String vId, FixType vFixType, String jId, FixType jFixType) { 25 | this.cdr3 = cdr3 26 | this.cdr3_old = cdr3_old 27 | this.fixNeeded = fixNeeded 28 | this.vId = vId 29 | this.vEnd = vEnd 30 | this.jStart = jStart 31 | this.vFixType = vFixType 32 | this.jFixType = jFixType 33 | this.jId = jId 34 | this.vCanonical = cdr3.startsWith("C") 35 | this.jCanonical = cdr3.endsWith("F") || cdr3.endsWith("W") 36 | } 37 | 38 | boolean isGood() { 39 | vFixType.good && jFixType.good 40 | } 41 | } 42 | -------------------------------------------------------------------------------- /src/KmerScanner.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | class KmerScanner { 18 | final int minHitSize 19 | final Map kmers = new HashMap<>(); 20 | 21 | KmerScanner(String seq, int minHitSize = 2) { 22 | this.minHitSize = minHitSize 23 | 24 | for (int i = minHitSize; i <= seq.length(); i++) { 25 | for (int j = 0; j <= seq.length() - i; j++) { 26 | String kmer = seq.substring(j, j + i) 27 | kmers.put(kmer, j) 28 | } 29 | } 30 | } 31 | 32 | SearchResult scan(String seq) { 33 | def bestHit = (minHitSize.. 34 | (0..<(seq.length() - i)).collect { int j -> 35 | String kmer = seq.substring(j, j + i) 36 | 37 | def hit = kmers[kmer] 38 | 39 | if (hit != null) { 40 | new SearchResult(hit, j, kmer.length()) 41 | } else { 42 | new SearchResult(-1, j, -1) 43 | } 44 | } 45 | }.flatten().max { it.matchSize } 46 | 47 | (bestHit && bestHit.matchSize > 0) ? bestHit : null 48 | 49 | /* 50 | // iterate from largest window to smallest one 51 | for (int i = seq.length(); i >= minHitSize; i--) { 52 | // sliding window scan 53 | for (int j = 0; j < seq.length() - i; j++) { 54 | String kmer = seq.substring(j, j + i) 55 | 56 | def hit = kmers[kmer] 57 | 58 | if (hit != null) { 59 | return new SearchResult(hit, 60 | j, 61 | kmer.length() 62 | ) 63 | } 64 | } 65 | } 66 | 67 | null*/ 68 | } 69 | } -------------------------------------------------------------------------------- /src/OneSideFixerResult.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | class OneSideFixerResult { 18 | final String cdr3 19 | final String segmentId 20 | final FixType fixType 21 | final int x 22 | 23 | OneSideFixerResult(String cdr3, String segmentId, FixType fixType, int x = -1) { 24 | this.cdr3 = cdr3 25 | this.segmentId = segmentId 26 | this.fixType = fixType 27 | this.x = x 28 | } 29 | } -------------------------------------------------------------------------------- /src/README.md: -------------------------------------------------------------------------------- 1 | This code runs database proofreading and assembly. Run as ``groovy -cp . BuildDatabase.groovy``. Requires Groovy, Python (+pandas). -------------------------------------------------------------------------------- /src/SearchResult.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | class SearchResult { 18 | final int startInSegment, startInCdr3, matchSize 19 | 20 | SearchResult(int startInSegment, int startInCdr3, int matchSize) { 21 | this.startInSegment = startInSegment 22 | this.startInCdr3 = startInCdr3 23 | this.matchSize = matchSize 24 | } 25 | } -------------------------------------------------------------------------------- /src/SlimComplexAccumulator.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | import groovy.json.JsonSlurper 18 | 19 | class SlimComplexAccumulator { 20 | static final List COMPLEX_SLIM_ANNOT_COLS = [ 21 | "gene", 22 | "cdr3", 23 | "species", 24 | "antigen.epitope", 25 | "antigen.gene", 26 | "antigen.species" 27 | ], SUMMARY_COLS = ["complex.id", 28 | "v.segm", "j.segm", 29 | "v.end", "j.start", 30 | "mhc.a", "mhc.b", "mhc.class", 31 | "reference.id", "vdjdb.score"] 32 | 33 | private static final JsonSlurper json = new JsonSlurper() 34 | 35 | final Set complexId = new HashSet<>(), 36 | vSegm = new HashSet<>(), 37 | jSegm = new HashSet<>(), 38 | mhcA = new HashSet<>(), 39 | mhcB = new HashSet<>(), 40 | mhcClass = new HashSet<>(), 41 | referenceId = new HashSet<>() 42 | 43 | int vdjdbScore = 0, vEnd = -1, jStart = -1 44 | 45 | SlimComplexAccumulator() { 46 | } 47 | 48 | void append(List splitLine, Map colIdMap) { 49 | complexId.addAll(splitLine[colIdMap["complex.id"]].split("[,;]").findAll { it.length() > 0 && it != "0" }) 50 | vSegm.addAll(splitLine[colIdMap["v.segm"]].split("[,;]").findAll { it.length() > 0 && it != "." }) 51 | jSegm.addAll(splitLine[colIdMap["j.segm"]].split("[,;]").findAll { it.length() > 0 && it != "." }) 52 | mhcA.addAll(splitLine[colIdMap["mhc.a"]].split("[,;]").findAll { it.length() > 0 && it != "." }) 53 | mhcB.addAll(splitLine[colIdMap["mhc.b"]].split("[,;]").findAll { it.length() > 0 && it != "." }) 54 | mhcClass.addAll(splitLine[colIdMap["mhc.class"]].split("[,;]").findAll { it.length() > 0 && it != "." }) 55 | referenceId.addAll(splitLine[colIdMap["reference.id"]].split("[,;]").findAll { it.length() > 0 && it != "." }) 56 | 57 | def fixData = json.parseText(splitLine[colIdMap["cdr3fix"]]) 58 | 59 | int vEnd1 = (int) fixData["vEnd"].toInteger(), 60 | jStart1 = (int) fixData["jStart"].toInteger() 61 | 62 | if (vEnd < 0 || vEnd < vEnd1) { 63 | vEnd = vEnd1 64 | } 65 | 66 | if (jStart < 0 || jStart > jStart1) { 67 | jStart = jStart1 68 | } 69 | 70 | vdjdbScore = Math.max(vdjdbScore, splitLine[colIdMap["vdjdb.score"]].toInteger()) 71 | } 72 | 73 | 74 | String getSummary() { 75 | [complexId.empty ? "0" : complexId.join(","), 76 | vSegm.join(","), 77 | jSegm.join(","), 78 | vEnd, 79 | jStart, 80 | mhcA.join(","), 81 | mhcB.join(","), 82 | mhcClass.join(","), 83 | referenceId.join(","), 84 | vdjdbScore].join("\t") 85 | } 86 | } 87 | -------------------------------------------------------------------------------- /src/Table.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | class Table implements Iterable { 18 | final List header 19 | final List rows 20 | final Map indices = new HashMap<>() 21 | 22 | Table(String[] header, List rows = []) { 23 | this.header = header.toList() 24 | this.rows = rows.collect { new Row(it) } 25 | 26 | header.eachWithIndex { String entry, int i -> 27 | indices[entry] = i 28 | } 29 | } 30 | 31 | void addCol(String colName) { 32 | indices[colName] = header.size() 33 | header << colName 34 | } 35 | 36 | void append(Table other) { 37 | other.rows.each { row -> 38 | def values = new String[header.size()] 39 | 40 | header.eachWithIndex { it, ind -> 41 | values[ind] = row[it] 42 | } 43 | 44 | rows << new Row(values) 45 | } 46 | } 47 | 48 | @Override 49 | Iterator iterator() { 50 | rows.iterator() 51 | } 52 | 53 | class Row { 54 | final List values 55 | 56 | Row(String[] values) { 57 | this.values = new ArrayList<>(values.length) 58 | 59 | values.each { this.values << it.trim() } 60 | } 61 | 62 | String getAt(String columnName) { 63 | values[indices[columnName]] 64 | } 65 | 66 | String putAt(String columnName, String value) { 67 | values[indices[columnName]] = value 68 | } 69 | } 70 | } 71 | -------------------------------------------------------------------------------- /src/Util.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | class Util { 18 | static String replaceNonAa(String seq) { 19 | seq.replaceAll(/[^FLSYCWPHQRIMTNKVADEG]/, "X") 20 | } 21 | 22 | static List simplifySegmentName(String segmentName) { 23 | def noAllele= segmentName.split("\\*")[0] 24 | [noAllele, noAllele.split("-")[0]] 25 | } 26 | 27 | static String codon2aa(String codon) { 28 | String codonUpper = codon.toUpperCase() 29 | switch (codonUpper) { 30 | case 'TTT': return 'F' 31 | case 'TTC': return 'F' 32 | case 'TTA': return 'L' 33 | case 'TTG': return 'L' 34 | case 'TCT': return 'S' 35 | case 'TCC': return 'S' 36 | case 'TCA': return 'S' 37 | case 'TCG': return 'S' 38 | case 'TAT': return 'Y' 39 | case 'TAC': return 'Y' 40 | case 'TAA': return '*' 41 | case 'TAG': return '*' 42 | case 'TGT': return 'C' 43 | case 'TGC': return 'C' 44 | case 'TGA': return '*' 45 | case 'TGG': return 'W' 46 | case 'CTT': return 'L' 47 | case 'CTC': return 'L' 48 | case 'CTA': return 'L' 49 | case 'CTG': return 'L' 50 | case 'CCT': return 'P' 51 | case 'CCC': return 'P' 52 | case 'CCA': return 'P' 53 | case 'CCG': return 'P' 54 | case 'CAT': return 'H' 55 | case 'CAC': return 'H' 56 | case 'CAA': return 'Q' 57 | case 'CAG': return 'Q' 58 | case 'CGT': return 'R' 59 | case 'CGC': return 'R' 60 | case 'CGA': return 'R' 61 | case 'CGG': return 'R' 62 | case 'ATT': return 'I' 63 | case 'ATC': return 'I' 64 | case 'ATA': return 'I' 65 | case 'ATG': return 'M' 66 | case 'ACT': return 'T' 67 | case 'ACC': return 'T' 68 | case 'ACA': return 'T' 69 | case 'ACG': return 'T' 70 | case 'AAT': return 'N' 71 | case 'AAC': return 'N' 72 | case 'AAA': return 'K' 73 | case 'AAG': return 'K' 74 | case 'AGT': return 'S' 75 | case 'AGC': return 'S' 76 | case 'AGA': return 'R' 77 | case 'AGG': return 'R' 78 | case 'GTT': return 'V' 79 | case 'GTC': return 'V' 80 | case 'GTA': return 'V' 81 | case 'GTG': return 'V' 82 | case 'GCT': return 'A' 83 | case 'GCC': return 'A' 84 | case 'GCA': return 'A' 85 | case 'GCG': return 'A' 86 | case 'GAT': return 'D' 87 | case 'GAC': return 'D' 88 | case 'GAA': return 'E' 89 | case 'GAG': return 'E' 90 | case 'GGT': return 'G' 91 | case 'GGC': return 'G' 92 | case 'GGA': return 'G' 93 | case 'GGG': return 'G' 94 | default: 95 | if (codonUpper.contains("N") && codonUpper.length() == 3) 96 | return "X" // undefined 97 | else 98 | return '?' // incomplete/missing 99 | } 100 | } 101 | 102 | static String translateLinear(String seq, boolean reverse) { 103 | def aaSeq = "" 104 | 105 | if (reverse) 106 | seq = seq.substring(seq.length() % 3) 107 | 108 | for (int i = 0; i <= seq.size() - 3; i += 3) { 109 | def codon = seq.substring(i, i + 3) 110 | aaSeq += codon2aa(codon) 111 | } 112 | 113 | aaSeq 114 | } 115 | } 116 | -------------------------------------------------------------------------------- /src/VdjdbScoreFactory.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright 2016-2017 Mikhail Shugay 3 | * 4 | * Licensed under the Apache License, Version 2.0 (the "License"); 5 | * you may not use this file except in compliance with the License. 6 | * You may obtain a copy of the License at 7 | * 8 | * http://www.apache.org/licenses/LICENSE-2.0 9 | * 10 | * Unless required by applicable law or agreed to in writing, software 11 | * distributed under the License is distributed on an "AS IS" BASIS, 12 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | * See the License for the specific language governing permissions and 14 | * limitations under the License. 15 | */ 16 | 17 | class VdjdbScoreFactory { 18 | final Map scoreMap = new HashMap<>() 19 | final Map> publicationMap = new HashMap<>() 20 | 21 | VdjdbScoreFactory(Table masterTable) { 22 | masterTable.each { row -> 23 | try { 24 | def sign = getSignature(row) 25 | 26 | // Assign publications 27 | def pubList = publicationMap[sign] 28 | if (pubList == null) { 29 | publicationMap.put(sign, pubList = new ArrayList()) 30 | } 31 | pubList << row["reference.id"] 32 | 33 | // Compute score 34 | def score 35 | if (row["meta.structure.id"].trim().length() > 0) { 36 | score = 3 // we have structure, any questions? :) 37 | } else { 38 | /* 39 | - We are sure that we have correct TCR sequence (+0 or +2) 40 | sanger - several cells sequenced (2+) 41 | single-cell - sure automatically 42 | amplicon-seq - frequency is higher than 0.01 43 | 44 | - We have moderate confidence about T-cell specificity (+0 or +2) 45 | sort-based method - frequency is higher than 0.1 46 | culture-based method - frequency is higher than 0.5 47 | limiting dilution/culture performed - frequency is higher than 0.5 48 | 49 | - We have high confidence about T-cell specificity (+0 or +3..+5) 50 | direct method - best 51 | stimulation-based - medium 52 | sort-based worst 53 | */ 54 | 55 | def freqStr = row["method.frequency"].trim() 56 | def freq = getFrequency(freqStr), 57 | count = getNumberOfCells(freqStr) 58 | 59 | assert freq <= 1.0f 60 | 61 | // sequencing 62 | def seqScore = 1 63 | 64 | def singleCell = row["method.singlecell"].trim().toLowerCase() 65 | 66 | if (singleCell.length() > 0 && singleCell != "no") { 67 | seqScore = 3 68 | } else { 69 | switch (row["method.sequencing"].trim().toLowerCase()) { 70 | case "sanger": 71 | seqScore = count >= 2 ? 3 : 2 72 | break 73 | case "amplicon-seq": 74 | seqScore = freq >= 0.01f ? 3 : 1 75 | break 76 | } 77 | } 78 | 79 | // Moderate confidence regarding specificity 80 | def identifyMethod = row["method.identification"].toLowerCase().trim() 81 | 82 | def specScore1 = 0 83 | 84 | if (cultureBasedIdentification(identifyMethod)) { 85 | specScore1 = freq >= 0.5f ? 1 : 0 86 | } else { 87 | if (sortBasedMethod(identifyMethod)) { 88 | specScore1 = freq >= 0.05f ? 1 : 0 89 | } else if (stimulationBasedMethod(identifyMethod)) { 90 | specScore1 = freq >= 0.25f ? 1 : 0 91 | } 92 | } 93 | 94 | // High confidence regarding specificity 95 | def verifyMethod = row["method.verification"].toLowerCase() 96 | 97 | def specScore2 = 0 98 | 99 | if (directVerification(verifyMethod)) { 100 | // A direct method to observe TCR specificity 101 | specScore2 = 3 102 | } else if (stimulationBasedMethod(verifyMethod)) { 103 | // Verification by target lysis, etc 104 | specScore2 = 2 105 | seqScore = 3 // tcr was cloned 106 | } else if (sortBasedMethod(verifyMethod)) { 107 | // Verification by cloning & re-staining 108 | specScore2 = 1 109 | seqScore = 3 // tcr was cloned 110 | } 111 | 112 | score = Math.min(seqScore, specScore1 + specScore2) 113 | } 114 | 115 | scoreMap[sign] = Math.max(scoreMap[sign] ?: 0, score) 116 | } catch (Exception e) { 117 | throw new RuntimeException("Error: " + e + "\nin " + 118 | row["reference.id"] + " " + row["cdr3.alpha"] + " " + row["cdr3.beta"]) 119 | } 120 | } 121 | } 122 | 123 | static int getNumberOfCells(String freq) { 124 | if (freq.length() == 0) { 125 | return 0 126 | } 127 | freq.contains('/') ? freq.split("/+")[0].toInteger() : 0 128 | } 129 | 130 | static float getFrequency(String freq) { 131 | if (freq.length() == 0) { 132 | return 0 133 | } 134 | if (freq.contains('/')) { 135 | def x = freq.split("/+").collect { it.toFloat() } 136 | return x[0] / x[1] 137 | } else if (freq.endsWith('%') && freq.length() > 1) { 138 | return freq[0..-2].toFloat() / 100.0f 139 | } else { 140 | return freq.toFloat() 141 | } 142 | } 143 | 144 | static boolean sortBasedMethod(String method) { 145 | // Sorting, magnetic separation, etc 146 | method.contains("sort") || method.contains("beads") || 147 | method.contains("separation") || method.contains("stain") 148 | } 149 | 150 | static boolean stimulationBasedMethod(String method) { 151 | // Indentification / verification by cloning with ag-loaded target cells, etc 152 | method.contains("targets") 153 | } 154 | 155 | static boolean cultureBasedIdentification(String method) { 156 | // Cultured prior to sequencing => frequency doesn't tell much 157 | method.contains("culture") || method.contains("cloning") 158 | } 159 | 160 | static boolean directVerification(String method) { 161 | // Verification by direct monitoring of pMHC binding 162 | method.contains("direct") 163 | } 164 | 165 | static final List SIGNATURE_COLS = [ 166 | "cdr3.alpha", 167 | "v.alpha", 168 | "j.alpha", 169 | "cdr3.beta", 170 | "v.beta", 171 | "j.beta", 172 | "species", 173 | "mhc.a", 174 | "mhc.b", 175 | "mhc.class", 176 | "antigen.epitope" 177 | ] 178 | 179 | int getScore(Table.Row row) { 180 | scoreMap[getSignature(row)] ?: 0 181 | } 182 | 183 | int getSamplesDetected(Table.Row row) { 184 | (publicationMap[getSignature(row)] ?: []).size() 185 | } 186 | 187 | int getStudiesDetected(Table.Row row) { 188 | (publicationMap[getSignature(row)] ?: []).unique().size() 189 | } 190 | 191 | String getSignature(Table.Row row) { 192 | SIGNATURE_COLS.collect { row[it] }.join("\t") 193 | } 194 | } 195 | -------------------------------------------------------------------------------- /summary/MakeEmbedableHtml.groovy: -------------------------------------------------------------------------------- 1 | def ignore = true, ignore2 = false 2 | new File("vdjdb_summary_embed.html").withPrintWriter { pw -> 3 | new File("vdjdb_summary.html").eachLine { line -> 4 | if (line.contains("!summary_embed_end!")) { 5 | ignore = true 6 | ignore2 = false 7 | } 8 | if (!ignore && line.contains("
")) {
 9 |         ignore2 = true
10 |     }
11 |     if (!ignore && !ignore2 && !line.startsWith("##")) {
13 |             line = line.replaceAll("#", "").replaceAll(""", "")
14 |         }
15 |         pw.println(line.replaceAll("", "
")
16 |                        .replaceAll(/width\s*=\s*"\d+"/, "width=\"100%\""))
17 |     }
18 |     if (line.contains("!summary_embed_start!")) {
19 |         ignore = false
20 |         ignore2 = false
21 |     }
22 |     if (!ignore && ignore2 && line.contains("")) {
23 |         ignore2 = false
24 |     }
25 | }
26 | }
27 | 


--------------------------------------------------------------------------------
/template.xls:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/antigenomics/vdjdb-db/4fe22b7969d0ab8c6910bbdce51c06f1f33679ea/template.xls


--------------------------------------------------------------------------------
/test.sh:
--------------------------------------------------------------------------------
1 | cd src/
2 | groovy -cp . BuildDatabase.groovy --no2fix


--------------------------------------------------------------------------------
/withheld/PMID_18799721.txt:
--------------------------------------------------------------------------------
1 | cdr3.alpha	v.alpha	j.alpha	cdr3.beta	v.beta	d.beta	j.beta	species	mhc.a	mhc.b	mhc.class	antigen.epitope	antigen.gene	antigen.species	reference.id	submitter	optional columns that ensure correct confidence ranking of a given entry. Used to calculate a single confidence score, similar to transcript confidence level in ENSEMBL	method.identification	method.frequency	method.singlecell	method.sequencing	method.verification	optional columns	meta.study.id	meta.cell.subset	meta.subset.frequency	meta.subject.cohort	meta.subject.id	meta.replica.id	meta.clone.id	meta.epitope.id	meta.tissue	meta.donor.MHC	meta.donor.MHC.method	meta.structure.id	comment
2 | CASSLEQHTEAFF			TRBJ1-1	HomoSapiens			MHCI	NLVPMVATV	pp65	CMV	PMID:18799721	Ekaterina Komech		antigen loaded targets, IFNg MACS / FACS			sanger	antigen loaded targets, IFNg CTL generation			CD3+CD8+CD69+IFNg+		healthy, CMV-seropositive	    1				PBMC	HLA-A*02			CTL lines based on IFNg assay
3 | CASSSRQGADTGELFF			TRBJ2-2	HomoSapiens			MHCI	NLVPMVATV	pp65	CMV	PMID:18799721	Ekaterina Komech		antigen loaded targets, IFNg MACS / FACS			sanger	antigen loaded targets, IFNg CTL generation			CD3+CD8+CD69+IFNg+		healthy, CMV-seropositive	    4a				PBMC	HLA-A*02			CTL lines based on IFNg assay
4 | CASRGLSGLTEAFF			TRBJ1-1	HomoSapiens			MHCI	NLVPMVATV	pp65	CMV	PMID:18799721	Ekaterina Komech		antigen loaded targets, IFNg MACS / FACS			sanger	antigen loaded targets, IFNg CTL generation			CD3+CD8+CD69+IFNg+		healthy, CMV-seropositive	    4b				PBMC	HLA-A*02			CTL lines based on IFNg assay
5 | CASQGTAATNTGELFF			TRBJ2-2	HomoSapiens			MHCI	NLVPMVATV	pp65	CMV	PMID:18799721	Ekaterina Komech		antigen loaded targets, IFNg MACS / FACS			sanger	antigen loaded targets, IFNg CTL generation			CD3+CD8+CD69+IFNg+		healthy, CMV-seropositive	    5				PBMC	HLA-A*02			CTL lines based on IFNg assay
6 | CASSYQTGAAYGYTF	TRBV6-5		TRBJ1-2	HomoSapiens			MHCI	NLVPMVATV	pp65	CMV	PMID:18799721	Ekaterina Komech		antigen loaded targets, IFNg MACS / FACS			sanger	antigen loaded targets, IFNg CTL generation			CD3+CD8+CD69+IFNg+		healthy, CMV-seropositive	    19				PBMC	HLA-A*02			CTL lines based on IFNg assay
7 | CASKWGPANPEAFF	TRBV27		TRBJ1-1	HomoSapiens			MHCI	NLVPMVATV	pp65	CMV	PMID:18799721	Ekaterina Komech		antigen loaded targets, IFNg MACS / FACS			sanger	antigen loaded targets, IFNg CTL generation			CD3+CD8+CD69+IFNg+		healthy, CMV-seropositive	    28a				PBMC	HLA-A*02			CTL lines based on IFNg assay
8 | CASKQGAGGNTEAFF	TRBV27		TRBJ1-1	HomoSapiens			MHCI	NLVPMVATV	pp65	CMV	PMID:18799721	Ekaterina Komech		antigen loaded targets, IFNg MACS / FACS			sanger	antigen loaded targets, IFNg CTL generation			CD3+CD8+CD69+IFNg+		healthy, CMV-seropositive	    28b				PBMC	HLA-A*02			CTL lines based on IFNg assay
9 | 


--------------------------------------------------------------------------------
/withheld/PMID_27254288.txt:
--------------------------------------------------------------------------------
 1 | cdr3.alpha	v.alpha	j.alpha	cdr3.beta	v.beta	d.beta	j.beta	species	mhc.a	mhc.b	mhc.class	antigen.epitope	antigen.gene	antigen.species	reference.id	submitter	optional columns that ensure correct confidence ranking of a given entry. Used to calculate a single confidence score, similar to transcript confidence level in ENSEMBL	method.identification	method.frequency	method.singlecell	method.sequencing	method.verification	optional columns	meta.study.id	meta.cell.subset	meta.subset.frequency	meta.subject.cohort	meta.subject.id	meta.replica.id	meta.clone.id	meta.epitope.id	meta.tissue	meta.donor.MHC	meta.donor.MHC.method	meta.structure.id	comment
 2 | CATSDLGSGVGNEQFF	TRBV24-1		TRBJ2-1	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets	 		sanger				CD4 depleted		AS	Don 10.05				PBMC	HLA-B*27:05,notHLA-B*07	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
 3 | CATSDLGQGVGNEQFF	TRBV24-1		TRBJ2-1	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets	 		sanger				CD4 depleted		AS	Don 1.05				PBMC	HLA-B*27:05	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
 4 | CASSQDMGQNNEQFF	TRBV4-1		TRBJ2-1	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets	 		sanger				CD4 depleted		AS	Don 17.05				PBMC	HLA-B*27:05	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
 5 | CASSQETGSYEQYF	TRBV4-1		TRBJ2-7	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets	 		sanger				CD4 depleted		AS	Don 1.05.07				PBMC	HLA-B*27:05,HLA-B*07:02	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
 6 | CASSQETGSYEQYF	TRBV4-1		TRBJ2-7	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets	 		sanger				CD4 depleted		healthy	Don 2.07				PBMC	HLA-B*07	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
 7 | CASSQEGGTATYEQYF	TRBV4-1		TRBJ2-7	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets			sanger				CD4 depleted		healthy	Don 3.07				PBMC	HLA-B*07	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
 8 | CASSQETGIHTQYF	TRBV4-1		TRBJ2-3	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets			sanger				CD4 depleted		healthy	Don 4.07				PBMC	HLA-B*07	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
 9 | CASSQDGAGGSTDTQYF	TRBV4-1		TRBJ2-3	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets			sanger				CD4 depleted		AS	Don 10.05				PBMC	HLA-B*27:05,notHLA-B*07	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
10 | CASSEGQVPSKEQFF	TRBV18		TRBJ2-7	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets			sanger				CD4 depleted		AS	Don 15.05				PBMC	HLA-B*27:05	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
11 | CASSEDGENTDTQYF	TRBV2		TRBJ2-3	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets			sanger				CD4 depleted		AS	Don 15.05				PBMC	HLA-B*27:05	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
12 | CASSEGAGGSYNEQFF	TRBV6-1		TRBJ2-1	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets			sanger				CD4 depleted		AS	Don 10.05				PBMC	HLA-B*27:05,notHLA-B*07	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
13 | CASSLGTDTQYF	TRBV3-1		TRBJ2-3	HomoSapiens				RPPIFIRRL	EBNA3a	EBV	PMID:27254288	Ekaterina Komech		antigen-loaded-targets			sanger				CD4 depleted		AS	Don 2.05.07				PBMC	HLA-B*27:05,HLA-B*07	serological typing, genomic analysis		The HLA-B*27 subtype was determined by serological analysis using ME1 mAb (specificity: HLA-B*27; -B*07; -B*42; -B*67; -B*73 and -B*w22) and genomic analysis. The positivity to HLA-B*07 was checked by BB7.1 (specificity: HLA-B*07)
14 | 


--------------------------------------------------------------------------------
/withheld/PMID_7964506.txt:
--------------------------------------------------------------------------------
1 | cdr3.alpha	v.alpha	j.alpha	cdr3.beta	v.beta	d.beta	j.beta	species	mhc.a	mhc.b	mhc.class	antigen.epitope	antigen.gene	antigen.species	reference.id	submitter	method.identification	method.frequency	method.singlecell	method.sequencing	method.verification	meta.study.id	meta.cell.subset	meta.subset.frequency	meta.subject.cohort	meta.subject.id	meta.replica.id	meta.clone.id	meta.epitope.id	meta.tissue	meta.donor.MHC	meta.donor.MHC.method	meta.structure.id	comment
2 | CILPLAGG	TRAV26-2	TRAJ14	CASSLGQAYEQY	TRBV7-6		TRBJ2-7	HomoSapiens		B2M	MHCI	FLRGRAYGL	EBNA3	EBV	PMID:7964506	Ivan Zvyagin	antigen-expressing-target			sanger	specific lysis of peptide-pulsed cells or CTL-CTL killing				healthy, EBV-seropositive	IM		IM6		PBMC	A1,A11,B8,B51			V segments converted from Arden et al. naming, HLA-B8 converted to HLA-B*08
3 | CILPLAGG	TRAV26-2	TRAJ14	CASSLGQAYEQY	TRBV7-6		TRBJ2-7	HomoSapiens		B2M	MHCI	FLRGRAYGL	EBNA3	EBV	PMID:7964506	Ivan Zvyagin	antigen-expressing-target			sanger	specific lysis of peptide-pulsed cells or CTL-CTL killing				healthy, EBV-seropositive	LC		LC13		PBMC	A1,-,B8,B18			V segments converted from Arden et al. naming, HLA-B8 converted to HLA-B*08
4 | CILPLAGG	TRAV26-2	TRAJ14	CASSLGQAYEQY	TRBV7-6		TRBJ2-7	HomoSapiens		B2M	MHCI	FLRGRAYGL	EBNA3	EBV	PMID:7964506	Ivan Zvyagin	antigen-expressing-target			sanger	specific lysis of peptide-pulsed cells or CTL-CTL killing				healthy, EBV-seropositive	SC		SC17		PBMC	A1,A31,B8.B51			V segments converted from Arden et al. naming, HLA-B8 converted to HLA-B*08
5 | CILPLAGG	TRAV26-2	TRAJ14	CASSLGQAYEQY	TRBV7-6		TRBJ2-7	HomoSapiens		B2M	MHCI	FLRGRAYGL	EBNA3	EBV	PMID:7964506	Ivan Zvyagin	antigen-expressing-target			sanger	specific lysis of peptide-pulsed cells or CTL-CTL killing				healthy, EBV-seropositive	AS		AS1		PBMC	A1,B8			V segments converted from Arden et al. naming, HLA-B8 converted to HLA-B*08
6 | CILPLSGG	TRAV26-2	TRAJ14	CASSIGQAYEQY	TRBV7-6		TRBJ2-7	HomoSapiens		B2M	MHCI	FLRGRAYGL	EBNA3	EBV	PMID:7964506	Ivan Zvyagin	antigen-expressing-target			sanger	specific lysis of peptide-pulsed cells or CTL-CTL killing				healthy, EBV-seropositive	DD		DD1		PBMC	A1,A3,B8,B40			V segments converted from Arden et al. naming, HLA-B8 converted to HLA-B*08
7 | 


--------------------------------------------------------------------------------
/withheld/PMID_9971792.txt:
--------------------------------------------------------------------------------
 1 | cdr3.alpha	v.alpha	j.alpha	cdr3.beta	v.beta	d.beta	j.beta	species	mhc.a	mhc.b	mhc.class	antigen.epitope	antigen.gene	antigen.species	reference.id	submitter	optional columns that ensure correct confidence ranking of a given entry. Used to calculate a single confidence score, similar to transcript confidence level in ENSEMBL	method.identification	method.frequency	method.singlecell	method.sequencing	method.verification	optional columns	meta.study.id	meta.cell.subset	meta.subset.frequency	meta.subject.cohort	meta.subject.id	meta.replica.id	meta.clone.id	meta.epitope.id	meta.tissue	meta.donor.MHC	meta.donor.MHC.method	meta.structure.id	comment
 2 | 			CASMGNSAGANVLTF	TRBV19		TRBJ2-6	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	6/6		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	011			495–503 pp65	PBMC	A2 A9(23) B15(62) B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
 3 | 			CASSSANYGYTF	TRBV12		TRBJ1-2	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	7/14		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	011			495–503 pp65	PBMC	A2 A9(23) B15(62) B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
 4 | 			CASSSVSEAFF	TRBV12		TRBJ1-1	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	5/14		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	011			495–503 pp65	PBMC	A2 A9(23) B15(62) B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
 5 | 			CASSSVNEQFF	TRBV12		TRBJ2-1	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	2/14		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	011			495–503 pp65	PBMC	A2 A9(23) B15(62) B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
 6 | 			CASSSANYGYTF	TRBV12		TRBJ1-2	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	3/3		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	015			495–503 pp65	PBMC	A2 A3 B7 B7	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
 7 | 			CASSYQTGTGNYGYTF	TRBV6-5		TRBJ1-2	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	3/4		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	001			495–503 pp65	PBMC	A2 B12(44) B27	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
 8 | 			CASSYSGHVYEQYF	TRBV6-5		TRBJ2-7	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	1/4		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	001			495–503 pp65	PBMC	A2 B12(44) B27	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
 9 | 			CASRGQGFSYEQYF	TRBV6-5		TRBJ2-7	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	4/4		sanger	antigen-expressing-targets	 		CD16 depleted		HIV+, CMV-seropositive	h0009			495–503 pp65	PBMC	A2 A9(24) B15(62) B27	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
10 | 			CASSFLGLNEQFF	TRBV7		TRBJ2-1	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	2/2		sanger	antigen-expressing-targets	 		CD16 depleted		HIV+, CMV-seropositive	h0009			495–503 pp65	PBMC	A2 A9(24) B15(62) B27	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
11 | 			CASSLDIPSYNEQFF	TRBV7		TRBJ2-1	HomoSapiens				NLVPMVATV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	5/5		sanger	antigen-expressing-targets	 		CD16 depleted		HIV+, CMV-seropositive	h0018			495–503 pp65	PBMC	A2 A3 B7 B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
12 | CILRGGGADGLTF	TRAV26-2	TRAJ45	CASSLGGNLYEQYF	TRBV7-9		TRBJ2-7	HomoSapiens				EFFWDANDIY	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	9/9		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	011			511–525 pp65	PBMC	A2 A9(23) B15(62) B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
13 | 			CASSSHDTGGYNSPLHF	TRBV7-9		TRBJ1-6	HomoSapiens				TPRVTGGGAM	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	2/5		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	002			417–426 pp65	PBMC	A9(24) A19(33) B7 B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
14 | 			CASSFRDYGNYEQYF	TRBV7-9		TRBJ2-7	HomoSapiens				TPRVTGGGAM	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	3/5		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	002			417–426 pp65	PBMC	A9(24) A19(33) B7 B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
15 | CATVLRMDSSYKLIF	TRAV17	TRAJ31	CASSLIGVSSYNEQFF	TRBV7-9		TRBJ2-1	HomoSapiens				TPRVTGGGAM	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	3/3		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	016			417–426 pp65	PBMC	A3 A3 B7 B7	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
16 | 			CASSSHDRQGASSPLHF	TRBV7-9		TRBJ1-6	HomoSapiens				TPRVTGGGAM	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	1/1		sanger	antigen-expressing-targets	 		CD16 depleted		HIV+, CMV-seropositive	h0018			417–426 pp65	PBMC	A2 A3 B7 B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
17 | CAMREGMDSSYKLIF	TRAV14/DV4	TRAJ31	CASSLHDRGSRTEAFF	TRBV7-9		TRBJ1-1	HomoSapiens				TPRVTGGGAM	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	8/8		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	015			417–426 pp65	PBMC	A2 A3 B7 B7	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
18 | 			CASKVGAGGLYEQYF	TRBV27		TRBJ2-7	HomoSapiens				TPRVTGGGAM	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	1/1		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	015			417–426 pp65	PBMC	A2 A3 B7 B7	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
19 | 			CASSIGPALNTEAFF	TRBV27		TRBJ1-1	HomoSapiens				TPRVTGGGAM	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	5/5		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	009			417–426 pp65	PBMC	A2 A3 B7 B37	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
20 | 			CASSQAALAGFGYEQYF	TRBV4-1		TRBJ2-7	HomoSapiens				RPHERNGFTV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	3/3		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	015			265–274 pp65	PBMC	A2 A3 B7 B7	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
21 | 			CASSPARNTEAFF	TRBV4-3		TRBJ1-1	HomoSapiens				RPHERNGFTV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	1/1		sanger	antigen-expressing-targets	 		CD16 depleted		healthy, CMV-seropositive	016			265–274 pp65	PBMC	A3 A3 B7 B7	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
22 | 			CASSPSRNTEAFF	TRBV4-3		TRBJ1-1	HomoSapiens				RPHERNGFTV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	1/5		sanger	antigen-expressing-targets	 		CD16 depleted		HIV+, CMV-seropositive	h0018			265–274 pp65	PBMC	A2 A3 B7 B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
23 | 			CASSPHRNTEAFF	TRBV4-3		TRBJ1-1	HomoSapiens				RPHERNGFTV	pp65	CMV	PMID:9971792	Ekaterina Komech		antigen-loaded-targets	4/5		sanger	antigen-expressing-targets	 		CD16 depleted		HIV+, CMV-seropositive	h0018			265–274 pp65	PBMC	A2 A3 B7 B12(44)	serological typing		Formal single-cell clones and low dilution CTL microcultures	CMV+ sero
24 | 


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