├── .gitignore ├── LICENSE ├── README.md ├── analyses ├── activation-bead-titration │ ├── Activation bead titration results via flow and count.ipynb │ ├── flow.csv │ └── proliferation_assay.tsv ├── buffy-pbmc-tcell │ ├── Buffy - PBMC - T cell counts.ipynb │ └── counts.tsv ├── cas9-electroporation │ ├── Cas9 and CD4 sgRNA RNP Electroporation.ipynb │ └── flow-data.tsv ├── il2-titration │ ├── IL2 titration results from multiple assays.ipynb │ ├── il2-count-long.tsv │ ├── il2-flow-long.tsv │ ├── il2-flow.csv │ ├── il2-resazurin.tsv │ ├── il2-sigma-nih-counts.tsv │ └── il2-sigma-nih-flow.tsv ├── isolation-bead-titration │ ├── Isolation bead titration.ipynb │ └── cd3-cd4-cd8-stats.tsv ├── mrna-electroporation │ ├── .DS_Store │ ├── Donor-specific mRNA electroporation efficiency in unactivated cells.ipynb │ ├── GFP mRNA electroporation.ipynb │ ├── data.csv │ └── donor-difference │ │ ├── act_vs_unac-flow.tsv │ │ ├── gfp-titration.tsv │ │ ├── unactivated-flow.tsv │ │ └── unactivated-flow2.tsv ├── pbmc-direct-activation │ ├── PBMC direct actication flow and count.ipynb │ ├── pbmc-cd3.tsv │ └── pbmc-counts.tsv ├── plasmid-electroporation │ ├── OPT vs RPMI1640 and T vs R buffer.ipynb │ └── opt_vs_rmpi1640-r_vs_t-day3.csv ├── pre-post-activation-cell-counts │ ├── Cell counts pre- and post- activation.ipynb │ └── counts.tsv ├── resazurin-assay │ ├── Resazurin assay sanity check.ipynb │ └── d7-cell-titration-data.tsv └── tsubset-prevalence │ ├── T cell subset variance across donors.ipynb │ ├── cd3-cd4-cd8.tsv │ └── naive-eff-central-memory.tsv ├── conda.env └── cover.png /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | env/ 12 | build/ 13 | develop-eggs/ 14 | dist/ 15 | downloads/ 16 | eggs/ 17 | .eggs/ 18 | lib/ 19 | lib64/ 20 | parts/ 21 | sdist/ 22 | var/ 23 | wheels/ 24 | *.egg-info/ 25 | .installed.cfg 26 | *.egg 27 | 28 | # PyInstaller 29 | # Usually these files are written by a python script from a template 30 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 31 | *.manifest 32 | *.spec 33 | 34 | # Installer logs 35 | pip-log.txt 36 | pip-delete-this-directory.txt 37 | 38 | # Unit test / coverage reports 39 | htmlcov/ 40 | .tox/ 41 | .coverage 42 | .coverage.* 43 | .cache 44 | nosetests.xml 45 | coverage.xml 46 | *.cover 47 | .hypothesis/ 48 | 49 | # Translations 50 | *.mo 51 | *.pot 52 | 53 | # Django stuff: 54 | *.log 55 | local_settings.py 56 | 57 | # Flask stuff: 58 | instance/ 59 | .webassets-cache 60 | 61 | # Scrapy stuff: 62 | .scrapy 63 | 64 | # Sphinx documentation 65 | docs/_build/ 66 | 67 | # PyBuilder 68 | target/ 69 | 70 | # Jupyter Notebook 71 | .ipynb_checkpoints 72 | 73 | # pyenv 74 | .python-version 75 | 76 | # celery beat schedule file 77 | celerybeat-schedule 78 | 79 | # SageMath parsed files 80 | *.sage.py 81 | 82 | # dotenv 83 | .env 84 | 85 | # virtualenv 86 | .venv 87 | venv/ 88 | ENV/ 89 | 90 | # Spyder project settings 91 | .spyderproject 92 | .spyproject 93 | 94 | # Rope project settings 95 | .ropeproject 96 | 97 | # mkdocs documentation 98 | /site 99 | 100 | # mypy 101 | .mypy_cache/ 102 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. 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We also recommend that a 185 | file or class name and description of purpose be included on the 186 | same "printed page" as the copyright notice for easier 187 | identification within third-party archives. 188 | 189 | Copyright [yyyy] [name of copyright owner] 190 | 191 | Licensed under the Apache License, Version 2.0 (the "License"); 192 | you may not use this file except in compliance with the License. 193 | You may obtain a copy of the License at 194 | 195 | http://www.apache.org/licenses/LICENSE-2.0 196 | 197 | Unless required by applicable law or agreed to in writing, software 198 | distributed under the License is distributed on an "AS IS" BASIS, 199 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 200 | See the License for the specific language governing permissions and 201 | limitations under the License. 202 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Human Primary T Cells: A Practical Guide 2 | [![DOI](https://zenodo.org/badge/120860634.svg)](https://zenodo.org/badge/latestdoi/120860634) 3 | 4 | ![ORLY](./cover.png) 5 | 6 | ## Guide 7 | - Live document: [Human Primary T Cells: A Practical Guide](https://docs.google.com/document/d/1LIuLDXPm1L3KvsZwtrhaZtiUjZ3i3y74uN_FcEM-gqk/edit#) 8 | - Preprint (v1): https://peerj.com/preprints/26993/ 9 | - Protocols: https://www.protocols.io/view/human-primary-t-cells-a-practical-guide-quvdww6 10 | 11 | ## Notebooks 12 | - [Hundreds of millions of T cells can be isolated from a buffy coat sample 13 | ](analyses/buffy-pbmc-tcell/Buffy%20-%20PBMC%20-%20T%20cell%20counts.ipynb) 14 | - [The relative abundance of T subsets vary across donors](analyses/tsubset-prevalence/T%20cell%20subset%20variance%20across%20donors.ipynb) 15 | - [Activation is required to rapidly expand T cells in culture but cell counts barely increase throughout the activation process](analyses/pre-post-activation-cell-counts/Cell%20counts%20pre-%20and%20post-%20activation.ipynb) 16 | - Electroporation is a feasible method for genetically manipulating T cells 17 | - [Plasmid electroporation is inefficient and causes major cell death 18 | ](analyses/plasmid-electroporation/OPT%20vs%20RPMI1640%20and%20T%20vs%20R%20buffer.ipynb) 19 | - [mRNA electroporation is convenient for transiently expressing exogenous proteins](analyses/mrna-electroporation/GFP%20mRNA%20electroporation.ipynb) 20 | - [Cas9 RNP electroporation is a feasible technique to knockout a gene 21 | ](analyses/cas9-electroporation/Cas9%20%20and%20CD4%20sgRNA%20RNP%20Electroporation.ipynb) 22 | - Common T cell techniques can be optimized for cost 23 | - [Untouched T cell isolation kit contents can be titrated down without major efficiency loss](analyses/isolation-bead-titration/Isolation%20bead%20titration.ipynb) 24 | - [Using fewer anti-CD3 and -CD28 beads for activation doesn’t immediately compromise activated cell yield](analyses/activation-bead-titration/Activation%20bead%20titration%20results%20via%20flow%20and%20count.ipynb) 25 | - [IL2 supplement is not necessary for short-term T cell cultures during and after CD3/CD28-based activation](analyses/il2-titration/IL2%20titration%20results%20from%20multiple%20assays.ipynb) 26 | - [T cell isolation can be circumvented by culturing PBMCs with activation beads](analyses/pbmc-direct-activation/PBMC%20direct%20actication%20flow%20and%20count.ipynb) 27 | - [NIH’s reagent service provides access to highly standardized and cost-effective recombinant IL2](analyses/il2-titration/IL2%20titration%20results%20from%20multiple%20assays.ipynb) 28 | -------------------------------------------------------------------------------- /analyses/activation-bead-titration/flow.csv: -------------------------------------------------------------------------------- 1 | Sample,Bead:Cell ratio,Live cells/CD4+ CD8+ | Freq. of Parent (%),Live cells/CD4+ CD8- | Freq. of Parent (%),Live cells/CD4- CD8+ | Freq. of Parent (%),Live cells/CD4- CD8- | Freq. of Parent (%),Live cells/CD4+ CD8- | Mean (Comp-PE-A),Live cells/CD4- CD8+ | Mean (Comp-PE-A) 2 | 10.fcs,0:1,2.51,41,38.3,18.2,85.6,106 3 | 11.fcs,1:1,1.37,52.7,37,8.97,958,753 4 | 12.fcs,1:2,1.25,50.9,39.3,8.58,903,706 5 | 14.fcs,1:4,0.86,51.4,38,9.72,781,612 6 | 18.fcs,1:8,0.87,51.1,36.7,11.4,613,454 7 | 20.fcs,0:1,1.62,40.6,38.5,18.9,77.1,121 8 | 21.fcs,1:1,1.26,50.1,39.6,9.1,923,732 9 | 22.fcs,1:2,1.22,51.1,39,8.65,864,700 10 | 24.fcs,1:4,1.18,51.8,37.6,9.48,783,601 11 | 28.fcs,1:8,1.1,50.7,36.7,11.5,580,437 12 | 30.fcs,0:1,1.92,40.7,39.1,18.2,74,98.8 13 | 31.fcs,1:1,1.32,50.6,39.3,8.73,900,716 14 | 32.fcs,1:2,1.22,51.7,38.1,8.94,814,651 15 | 34.fcs,1:4,1.07,51.8,37.7,9.44,717,582 16 | 38.fcs,1:8,0.98,51.2,36.4,11.4,572,429 -------------------------------------------------------------------------------- /analyses/activation-bead-titration/proliferation_assay.tsv: -------------------------------------------------------------------------------- 1 | Row Donor 1:1 1:2 1:4 1:8 1:16 1:32 1:64 1:128 1:256 1:512 1:1024 1:2048 2 | A D8 0.253 0.232 0.219 0.22 0.185 0.174 0.151 0.135 0.122 0.126 0.115 0.115 3 | B D8 0.232 0.242 0.227 0.205 0.196 0.186 0.149 0.15 0.126 0.126 0.119 0.11 4 | C D8 0.229 0.226 0.218 0.212 0.177 0.171 0.151 0.133 0.118 0.114 0.119 0.118 5 | D D8 0.237 0.215 0.223 0.213 0.193 0.18 0.158 0.144 0.124 0.119 0.115 0.11 6 | E D8 0.235 0.229 0.226 0.207 0.198 0.183 0.166 0.15 0.137 0.122 0.12 0.119 7 | F D8 0.238 0.22 0.205 0.207 0.194 0.184 0.164 0.15 0.13 0.12 0.121 0.114 8 | G D8 0.247 0.242 0.213 0.217 0.201 0.176 0.157 0.145 0.131 0.121 0.12 0.119 9 | H D8 0.258 0.267 0.249 0.252 0.252 0.221 0.185 0.173 0.173 0.157 0.148 0.134 10 | A D9 0.221 0.204 0.207 0.213 0.211 0.181 0.17 0.148 0.128 0.121 0.121 0.123 11 | B D9 0.244 0.213 0.226 0.215 0.203 0.182 0.165 0.152 0.12 0.12 0.113 0.114 12 | C D9 0.242 0.219 0.212 0.201 0.185 0.162 0.15 0.129 0.11 0.11 0.109 0.114 13 | D D9 0.242 0.225 0.229 0.207 0.189 0.169 0.155 0.139 0.128 0.118 0.109 0.108 14 | E D9 0.235 0.226 0.227 0.213 0.201 0.177 0.166 0.145 0.138 0.129 0.119 0.119 15 | F D9 0.236 0.243 0.23 0.221 0.207 0.18 0.163 0.149 0.145 0.13 0.125 0.119 16 | G D9 0.235 0.226 0.22 0.224 0.193 0.189 0.164 0.145 0.142 0.13 0.128 0.122 17 | H D9 0.249 0.256 0.252 0.246 0.219 0.206 0.191 0.175 0.171 0.153 0.147 0.143 18 | -------------------------------------------------------------------------------- /analyses/buffy-pbmc-tcell/counts.tsv: -------------------------------------------------------------------------------- 1 | Donor PBMC count T cell count T cell / PBMC 2 | D3 1.35E+09 2.50E+08 18.52 3 | D4 3.50E+08 1.20E+08 34.29 4 | D7 7.50E+08 2.40E+08 32.00 5 | D8 6.40E+08 5.70E+08 89.06 6 | D9 6.00E+08 4.80E+08 80.00 7 | D14 1.00E+09 2.00E+08 20.00 8 | D15 7.60E+08 3.60E+08 47.37 9 | D16 5.40E+08 2.00E+08 37.04 10 | D17 6.70E+08 3.40E+08 50.75 11 | D20 8.80E+08 2.70E+08 30.68 12 | D21 1.00E+09 4.10E+08 41.00 13 | -------------------------------------------------------------------------------- /analyses/cas9-electroporation/Cas9 and CD4 sgRNA RNP Electroporation.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "metadata": {}, 7 | "outputs": [ 8 | { 9 | "name": "stderr", 10 | "output_type": "stream", 11 | "text": [ 12 | "\n", 13 | "Attaching package: ‘dplyr’\n", 14 | "\n", 15 | "The following objects are masked from ‘package:stats’:\n", 16 | "\n", 17 | " filter, lag\n", 18 | "\n", 19 | "The following objects are masked from ‘package:base’:\n", 20 | "\n", 21 | " intersect, setdiff, setequal, union\n", 22 | "\n", 23 | "\n", 24 | "Attaching package: ‘tidyr’\n", 25 | "\n", 26 | "The following object is masked from ‘package:magrittr’:\n", 27 | "\n", 28 | " extract\n", 29 | "\n" 30 | ] 31 | } 32 | ], 33 | "source": [ 34 | "library('readr')\n", 35 | "library('magrittr')\n", 36 | "library('dplyr')\n", 37 | "library('tidyr')\n", 38 | "library('ggplot2')" 39 | ] 40 | }, 41 | { 42 | "cell_type": "code", 43 | "execution_count": 10, 44 | "metadata": {}, 45 | "outputs": [ 46 | { 47 | "data": { 48 | "text/html": [ 49 | "\n", 50 | "\n", 51 | "\n", 52 | "\t\n", 53 | "\t\n", 54 | "\t\n", 55 | "\t\n", 56 | "\n", 57 | "
DonorsgRNAavg_cd4sd_cd4
Donor 14 None 78.566667 6.726316
Donor 14 CD4 9.806667 1.035197
Donor 15 None 83.20000011.171840
Donor 15 CD4 11.666667 1.607275
\n" 58 | ], 59 | "text/latex": [ 60 | "\\begin{tabular}{r|llll}\n", 61 | " Donor & sgRNA & avg\\_cd4 & sd\\_cd4\\\\\n", 62 | "\\hline\n", 63 | "\t Donor 14 & None & 78.566667 & 6.726316\\\\\n", 64 | "\t Donor 14 & CD4 & 9.806667 & 1.035197\\\\\n", 65 | "\t Donor 15 & None & 83.200000 & 11.171840\\\\\n", 66 | "\t Donor 15 & CD4 & 11.666667 & 1.607275\\\\\n", 67 | "\\end{tabular}\n" 68 | ], 69 | "text/markdown": [ 70 | "\n", 71 | "Donor | sgRNA | avg_cd4 | sd_cd4 | \n", 72 | "|---|---|---|---|\n", 73 | "| Donor 14 | None | 78.566667 | 6.726316 | \n", 74 | "| Donor 14 | CD4 | 9.806667 | 1.035197 | \n", 75 | "| Donor 15 | None | 83.200000 | 11.171840 | \n", 76 | "| Donor 15 | CD4 | 11.666667 | 1.607275 | \n", 77 | "\n", 78 | "\n" 79 | ], 80 | "text/plain": [ 81 | " Donor sgRNA avg_cd4 sd_cd4 \n", 82 | "1 Donor 14 None 78.566667 6.726316\n", 83 | "2 Donor 14 CD4 9.806667 1.035197\n", 84 | "3 Donor 15 None 83.200000 11.171840\n", 85 | "4 Donor 15 CD4 11.666667 1.607275" 86 | ] 87 | }, 88 | 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w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\ntD0ejB8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185 | "text/plain": [ 186 | "plot without title" 187 | ] 188 | }, 189 | "metadata": {}, 190 | "output_type": "display_data" 191 | } 192 | ], 193 | "source": [ 194 | "ko_summary %>%\n", 195 | "ggplot(aes(x=`sgRNA`, y=`avg_cd4`, fill=`sgRNA`)) +\n", 196 | " geom_col() +\n", 197 | " geom_errorbar(aes(\n", 198 | " ymin=`avg_cd4`-`sd_cd4`,\n", 199 | " ymax=`avg_cd4`+`sd_cd4`\n", 200 | " ), width=.2) +\n", 201 | " facet_wrap(~Donor, ncol=2) +\n", 202 | " ylab('Percent CD4+ Population (%)\\n(n=3)') +\n", 203 | " ylim(0, 100)" 204 | ] 205 | } 206 | ], 207 | "metadata": { 208 | "kernelspec": { 209 | "display_name": "R", 210 | "language": "R", 211 | "name": "ir" 212 | }, 213 | "language_info": { 214 | "codemirror_mode": "r", 215 | "file_extension": ".r", 216 | "mimetype": "text/x-r-source", 217 | "name": "R", 218 | "pygments_lexer": "r", 219 | "version": "3.4.1" 220 | } 221 | }, 222 | "nbformat": 4, 223 | "nbformat_minor": 2 224 | } 225 | -------------------------------------------------------------------------------- /analyses/cas9-electroporation/flow-data.tsv: -------------------------------------------------------------------------------- 1 | Donor Replicate sgRNA Live/CD4+ CD8+ | Freq. of Parent Live/CD4+ CD8- | Freq. of Parent Live/CD4+ CD8-/CD25+ | Freq. of Parent Live/CD4+ CD8-/CD25- | Freq. of Parent Live/CD4- CD8+ | Freq. of Parent Live/CD4- CD8+/CD25+ | Freq. of Parent Live/CD4- CD8+/CD25- | Freq. of Parent Live/CD4- CD8- | Freq. of Parent Live/CD25+ | Freq. of Parent Live/CD25- | Freq. of Parent 2 | D14 R1 N/A 2.07 70.8 82.1 17.9 11.9 90.4 9.57 15.2 82.2 17.8 3 | D14 R2 N/A 2.38 82.5 66 17.2 12.7 90.4 9.62 2.45 83.7 16.3 4 | D14 R3 N/A 2.28 82.4 86.9 13.1 12.1 91.3 8.73 3.19 87 13 5 | D15 R1 N/A 1.61 76.7 77.2 22.8 18.6 84.3 15.7 3.11 78.4 21.6 6 | D15 R2 N/A 1.84 76.8 79.3 20.7 18 85.6 14.4 3.26 80.3 19.7 7 | D15 R3 N/A 2.35 96.1 77.4 22.6 22.4 84.5 15.5 4.07 104 20.5 8 | D14 R1 CD4 0.18 9.27 78.8 21.2 14.7 89.8 10.2 75.8 87.2 12.8 9 | D14 R2 CD4 0.28 9.15 77.8 22.2 14.7 88.7 11.3 75.9 86.3 13.7 10 | D14 R3 CD4 0.28 11 74.5 25.5 13.9 88.5 11.5 74.8 85 15 11 | D15 R1 CD4 0.46 10.5 67.4 32.6 18.8 84.9 15.1 70.2 82 18 12 | D15 R2 CD4 0.46 11 64.8 35.2 18.5 81.7 18.3 70.1 78 22 13 | D15 R3 CD4 0.36 13.5 61.2 38.8 17.9 77.2 22.8 68.3 74.1 25.9 14 | -------------------------------------------------------------------------------- /analyses/il2-titration/il2-count-long.tsv: -------------------------------------------------------------------------------- 1 | Donor Day Condition Replicate Count No Live count Live Fraction Dilution 2 | D14 5 +IL2 r1 1 1.05E+06 0.62 1 3 | D14 5 +IL2 r1 2 1.10E+06 0.63 1 4 | D14 5 +IL2 r2 1 1.25E+06 0.75 1 5 | D14 5 +IL2 r2 2 2.17E+05 0.11 1 6 | D14 5 +IL2 r3 1 1.13E+06 0.7 1 7 | D14 5 +IL2 r3 2 1.16E+06 0.64 1 8 | D14 5 -IL2 r1 1 1.08E+06 0.65 1 9 | D14 5 -IL2 r1 2 9.15E+05 0.63 1 10 | D14 5 -IL2 r2 1 1.51E+06 0.37 1 11 | D14 5 -IL2 r2 2 1.14E+06 0.68 1 12 | D14 5 -IL2 r3 1 1.21E+06 0.64 1 13 | D14 5 -IL2 r3 2 1.22E+06 0.71 1 14 | D15 5 +IL2 r1 1 4.63E+05 0.18 1 15 | D15 5 +IL2 r1 2 1.11E+06 0.72 1 16 | D15 5 +IL2 r2 1 1.62E+06 0.73 1 17 | D15 5 +IL2 r2 2 2.21E+06 0.73 1 18 | D15 5 +IL2 r3 1 1.22E+06 0.74 1 19 | D15 5 +IL2 r3 2 1.54E+06 0.75 1 20 | D15 5 -IL2 r1 1 1.04E+06 0.75 1 21 | D15 5 -IL2 r1 2 1.05E+06 0.73 1 22 | D15 5 -IL2 r2 1 1.33E+06 0.72 1 23 | D15 5 -IL2 r2 2 1.37E+06 0.73 1 24 | D15 5 -IL2 r3 1 1.30E+06 0.74 1 25 | D15 5 -IL2 r3 2 1.05E+06 0.69 1 26 | D14 8 +IL2 r1 1 4.16E+05 0.61 3 27 | D14 8 +IL2 r1 2 3.75E+05 0.5 3 28 | D14 8 +IL2 r2 1 6.16E+05 0.56 3 29 | D14 8 +IL2 r2 2 5.10E+05 0.61 3 30 | D14 8 +IL2 r3 1 4.34E+05 0.53 3 31 | D14 8 +IL2 r3 2 3.64E+05 0.49 3 32 | D14 8 -IL2 r1 1 2.99E+05 0.44 3 33 | D14 8 -IL2 r1 2 3.46E+05 0.54 3 34 | D14 8 -IL2 r2 1 4.11E+05 0.71 3 35 | D14 8 -IL2 r2 2 3.40E+05 0.51 3 36 | D14 8 -IL2 r3 1 4.16E+05 0.5 3 37 | D14 8 -IL2 r3 2 4.22E+05 0.55 3 38 | D15 8 +IL2 r1 1 4.93E+05 0.64 3 39 | D15 8 +IL2 r1 2 4.22E+05 0.62 3 40 | D15 8 +IL2 r2 1 5.40E+05 0.7 3 41 | D15 8 +IL2 r2 2 6.22E+05 0.68 3 42 | D15 8 +IL2 r3 1 5.34E+05 0.58 3 43 | D15 8 +IL2 r3 2 4.28E+05 0.56 3 44 | D15 8 -IL2 r1 1 3.64E+05 0.48 3 45 | D15 8 -IL2 r1 2 2.82E+05 0.42 3 46 | D15 8 -IL2 r2 1 4.46E+05 0.55 3 47 | D15 8 -IL2 r2 2 4.87E+05 0.49 3 48 | D15 8 -IL2 r3 1 4.05E+05 0.46 3 49 | D15 8 -IL2 r3 2 3.93E+05 0.5 3 -------------------------------------------------------------------------------- /analyses/il2-titration/il2-flow-long.tsv: -------------------------------------------------------------------------------- 1 | Replicate Day Donor Condition Live/CD4+ CD8+ | Freq. of Parent Live/CD4+ CD8- | Freq. of Parent Live/CD4+ CD8-/CD25+ | Freq. of Parent Live/CD4+ CD8-/CD25- | Freq. of Parent Live/CD4- CD8+ | Freq. of Parent Live/CD4- CD8+/CD25+ | Freq. of Parent Live/CD4- CD8+/CD25- | Freq. of Parent Live/CD4- CD8- | Freq. of Parent Live/CD25+ | Freq. of Parent 2 | r1 5 D14 -IL2 2.6 77.9 87.1 12.9 11.4 86.2 13.8 8.08 86 3 | r2 5 D14 -IL2 2.47 77.7 86.8 13.2 11.4 85.7 14.3 8.5 85.6 4 | r3 5 D14 -IL2 2.41 76.8 87.1 12.9 11.6 85.5 14.5 9.11 85.7 5 | r1 5 D14 +IL2 2.23 77.5 86.8 13.2 11.3 86.1 13.9 8.91 85.4 6 | r2 5 D14 +IL2 2.47 80.1 86.2 13.8 11.3 86.5 13.5 6.17 85.3 7 | r3 5 D14 +IL2 2.35 78.3 87.1 12.9 11.5 86.7 13.3 7.82 85.9 8 | r1 5 D15 -IL2 1.86 73.4 86.3 13.7 16.6 84.9 15.1 8.12 85.2 9 | r2 5 D15 -IL2 1.87 72.5 86.8 13.2 16.5 83.2 16.8 9.19 85.4 10 | r3 5 D15 -IL2 1.96 73 86 14 16.3 83.2 16.8 8.77 84.7 11 | r1 5 D15 +IL2 1.56 72.2 85.7 14.3 16.8 83.3 16.7 9.42 84.3 12 | r2 5 D15 +IL2 1.66 74.3 85.8 14.2 16.3 85 15 7.71 85 13 | r3 5 D15 +IL2 1.76 73.4 86 14 15.9 83.1 16.9 8.95 84.7 14 | r1 8 D14 -IL2 12.4 78.7 52.9 47.1 6.42 55.8 44.2 2.8 54.3 15 | r2 8 D14 -IL2 11.8 80.5 52.4 47.6 5.77 58.1 41.9 2.26 54.5 16 | r3 8 D14 -IL2 12 79.8 53.4 46.6 6.16 59.2 40.8 2.41 55.1 17 | r1 8 D14 +IL2 11.3 80.2 52.6 47.4 5.54 55 45 3.28 54.1 18 | r2 8 D14 +IL2 11.7 80.5 53.2 46.8 5.55 57.5 42.5 2.51 54.5 19 | r3 8 D14 +IL2 11.8 81.2 51.5 48.5 5.38 56.6 43.4 1.85 53.5 20 | r1 8 D15 -IL2 9.61 84.6 43.9 56.1 4.73 29.4 70.6 1.33 43.4 21 | r2 8 D15 -IL2 9.79 84.4 45.1 54.9 4.92 29.4 70.6 1.16 44.3 22 | r3 8 D15 -IL2 10 84.8 43.1 56.9 4.29 33.4 66.6 1.09 43.1 23 | r1 8 D15 +IL2 9.3 85.1 44.8 55.2 4.57 30.6 69.4 1.35 44 24 | r2 8 D15 +IL2 8.98 85.8 42.5 57.5 4.44 29.5 70.5 1.04 42.1 25 | r3 8 D15 +IL2 9.92 84.4 42.1 57.9 4.51 26.3 73.7 1.44 41.5 26 | -------------------------------------------------------------------------------- /analyses/il2-titration/il2-flow.csv: -------------------------------------------------------------------------------- 1 | Sample,Replicate,IL2,Live cells/CD4+ CD8+ | Freq. of Parent (%),Live cells/CD4+ CD8- | Freq. of Parent (%),Live cells/CD4- CD8+ | Freq. of Parent (%),Live cells/CD4- CD8- | Freq. of Parent (%),Live cells/CD4+ CD8+ | Mean (Comp-PE-A),Live cells/CD4+ CD8- | Mean (Comp-PE-A),Live cells/CD4- CD8+ | Mean (Comp-PE-A),Live cells/CD4- CD8- | Mean (Comp-PE-A) 2 | 11.fcs,R1,512,1.61,46,39.8,12.6,1545,1067,812,528 3 | 12.fcs,R1,256,1.73,49.8,39,9.53,1117,1053,804,504 4 | 13.fcs,R1,128,1.66,49.3,39.6,9.42,1106,1066,833,509 5 | 14.fcs,R1,64,1.97,48.8,39.6,9.63,1484,998,764,490 6 | 15.fcs,R1,32,1.94,48.8,39.7,9.57,1326,1057,831,513 7 | 16.fcs,R1,0,1.85,48.4,39.8,9.88,1322,1003,774,501 8 | 21.fcs,R1,512,1.59,60.5,50.6,12.2,1104,1099,839,515 9 | 22.fcs,R1,256,1.41,49.3,39.4,9.87,1951,1075,828,500 10 | 23.fcs,R1,128,1.69,48.8,39.7,9.78,1179,1072,834,511 11 | 24.fcs,R1,64,1.8,48.8,39.7,9.65,1222,1041,821,504 12 | 25.fcs,R1,32,1.77,48.7,39.4,10.1,1302,1052,807,501 13 | 26.fcs,R1,0,1.32,49.5,39.6,9.6,1468,1085,832,520 14 | 31.fcs,R1,512,1.45,48.6,39.7,10.3,1059,1018,792,483 15 | 32.fcs,R1,256,1.79,48.9,39.5,9.81,1392,1052,816,495 16 | 33.fcs,R1,128,1.5,49.5,39.1,9.91,1157,1073,849,511 17 | 34.fcs,R1,64,1.79,49.4,38.6,10.1,1247,1057,795,489 18 | 35.fcs,R1,32,1.5,48.9,39.8,9.84,1143,1042,810,489 19 | 36.fcs,R1,0,1.58,50,38.4,9.99,1008,980,749,469 20 | 41.fcs,R1,512,1.59,48.9,39.3,10.2,1255,985,755,488 21 | 42.fcs,R1,256,1.45,50.2,38.2,10.2,1252,1040,778,512 22 | 43.fcs,R1,128,1.62,50.3,37.9,10.1,1477,1057,803,487 23 | 44.fcs,R1,64,1.39,49.7,38.5,10.4,1537,999,758,471 24 | 45.fcs,R1,32,1.6,49.7,38.5,10.2,1441,1022,778,476 25 | 46.fcs,R1,0,1.39,49.5,38.9,10.2,1707,1038,812,476 -------------------------------------------------------------------------------- /analyses/il2-titration/il2-resazurin.tsv: -------------------------------------------------------------------------------- 1 | Row C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 Replicate 2 | A 0.327 0.415 0.48 0.388 0.465 0.375 0.401 0.38 0.395 0.398 0.433 0.423 R1 3 | B 0.439 0.399 0.466 0.374 0.476 0.429 0.424 0.487 0.457 0.465 0.427 0.393 R1 4 | C 0.439 0.448 0.451 0.448 0.438 0.434 0.455 0.445 0.45 0.4 0.381 0.4 R1 5 | D 0.459 0.441 0.461 0.504 0.459 0.41 0.468 0.408 0.408 0.399 0.376 0.375 R1 6 | E 0.424 0.429 0.503 0.479 0.535 0.465 0.473 0.414 0.409 0.394 0.413 0.426 R1 7 | F 0.436 0.434 0.457 0.425 0.468 0.461 0.486 0.46 0.458 0.363 0.481 0.377 R1 8 | G 0.432 0.459 0.482 0.46 0.459 0.486 0.466 0.462 0.385 0.387 0.4 0.376 R1 9 | H 0.405 0.445 0.447 0.442 0.477 0.49 0.413 0.441 0.437 0.391 0.374 0.406 R1 10 | A 0.424 0.431 0.433 0.434 0.444 0.43 0.435 0.44 0.438 0.442 0.433 0.439 R2 11 | B 0.428 0.427 0.433 0.429 0.436 0.436 0.437 0.437 0.436 0.441 0.436 0.437 R2 12 | C 0.423 0.425 0.433 0.437 0.434 0.43 0.435 0.434 0.437 0.435 0.43 0.45 R2 13 | D 0.439 0.428 0.436 0.436 0.435 0.443 0.436 0.45 0.436 0.422 0.436 0.44 R2 14 | E 0.418 0.421 0.428 0.434 0.419 0.428 0.452 0.424 0.436 0.4 0.424 0.438 R2 15 | F 0.431 0.423 0.429 0.427 0.422 0.42 0.424 0.426 0.431 0.404 0.428 0.432 R2 16 | G 0.425 0.419 0.427 0.422 0.414 0.413 0.399 0.437 0.433 0.403 0.427 0.438 R2 17 | H 0.41 0.403 0.4 0.431 0.422 0.414 0.426 0.433 0.411 0.395 0.416 0.422 R2 18 | A 0.253 0.229 0.216 0.208 0.216 0.211 0.223 0.231 0.215 0.213 0.228 0.208 R3 19 | B 0.231 0.221 0.231 0.217 0.223 0.222 0.216 0.207 0.201 0.213 0.205 0.209 R3 20 | C 0.232 0.212 0.218 0.218 0.216 0.214 0.209 0.205 0.205 0.202 0.205 0.216 R3 21 | D 0.226 0.217 0.214 0.218 0.214 0.207 0.21 0.207 0.202 0.192 0.197 0.202 R3 22 | E 0.229 0.219 0.222 0.217 0.22 0.221 0.211 0.22 0.217 0.204 0.202 0.217 R3 23 | F 0.222 0.223 0.214 0.222 0.209 0.218 0.208 0.205 0.205 0.202 0.202 0.218 R3 24 | G 0.22 0.214 0.223 0.222 0.211 0.208 0.201 0.205 0.204 0.2 0.215 0.216 R3 25 | H 0.246 0.234 0.235 0.24 0.25 0.251 0.214 0.236 0.243 0.203 0.232 0.236 R3 26 | A 0.506 0.453 0.434 0.446 0.427 0.427 0.445 0.473 0.444 0.434 0.466 0.45 R4 27 | B 0.449 0.435 0.469 0.46 0.448 0.481 0.435 0.455 0.461 0.462 0.442 0.454 R4 28 | C 0.497 0.439 0.477 0.456 0.467 0.425 0.432 0.458 0.457 0.456 0.454 0.473 R4 29 | D 0.446 0.433 0.443 0.453 0.446 0.47 0.451 0.457 0.427 0.434 0.434 0.444 R4 30 | E 0.476 0.453 0.466 0.473 0.471 0.437 0.424 0.487 0.441 0.417 0.438 0.513 R4 31 | F 0.478 0.437 0.442 0.447 0.445 0.447 0.429 0.433 0.44 0.417 0.454 0.457 R4 32 | G 0.507 0.43 0.435 0.451 0.439 0.427 0.471 0.442 0.443 0.462 0.485 0.446 R4 33 | H 0.423 0.412 0.424 0.496 0.447 0.453 0.467 0.447 0.457 0.363 0.46 0.468 R4 34 | -------------------------------------------------------------------------------- /analyses/il2-titration/il2-sigma-nih-counts.tsv: -------------------------------------------------------------------------------- 1 | donor id IL-2 conct live count (cells/ml) live % size (um) IL2 Source Replicate 2 | 4 500 500000 87 14.23 Sigma R1 3 | 4 500 500000 74 13.59 Sigma R2 4 | 4 250 628000 89 13.78 Sigma R1 5 | 4 250 581000 86 14.13 Sigma R2 6 | 4 125 457000 81 13.22 Sigma R1 7 | 4 125 405000 85 13.54 Sigma R2 8 | 4 64 475000 82 13.64 Sigma R1 9 | 4 64 551000 87 14.87 Sigma R2 10 | 4 32 581000 88 14.67 Sigma R1 11 | 4 32 581000 81 14.03 Sigma R2 12 | 4 0 569000 86 13.97 Sigma R1 13 | 4 0 598000 81 13.7 Sigma R2 14 | 15 500 446000 75 13.12 Sigma R1 15 | 15 500 416000 73 12.77 Sigma R2 16 | 15 250 334000 73 12.37 Sigma R1 17 | 15 250 364000 76 13.5 Sigma R2 18 | 15 125 328000 73 12.82 Sigma R1 19 | 15 125 387000 71 14.3 Sigma R2 20 | 15 64 93800 16 9.54 Sigma R1 21 | 15 64 422000 74 13.08 Sigma R2 22 | 15 32 240000 61 12.83 Sigma R1 23 | 15 32 299000 61 12.55 Sigma R2 24 | 15 0 299000 71 12.01 Sigma R1 25 | 15 0 264000 71 12.91 Sigma R2 26 | 16 500 528000 91 14.37 Sigma R1 27 | 16 500 510000 91 14.69 Sigma R2 28 | 16 250 493000 89 14.83 Sigma R1 29 | 16 250 428000 87 15.53 Sigma R2 30 | 16 125 522000 93 14.53 Sigma R1 31 | 16 125 469000 95 16.06 Sigma R2 32 | 16 64 469000 94 14.54 Sigma R1 33 | 16 64 422000 94 14.36 Sigma R2 34 | 16 32 457000 91 14.19 Sigma R1 35 | 16 32 405000 93 14 Sigma R2 36 | 16 0 557000 91 13.97 Sigma R1 37 | 16 0 479000 94 14.58 Sigma R2 38 | 17 500 352000 88 13.8 Sigma R1 39 | 17 500 270000 87 13.93 Sigma R2 40 | 17 250 499000 88 13.59 Sigma R1 41 | 17 250 422000 87 14.57 Sigma R2 42 | 17 125 381000 82 13.89 Sigma R1 43 | 17 125 416000 93 15.14 Sigma R2 44 | 17 64 452000 94 14.31 Sigma R1 45 | 17 64 422000 90 14.04 Sigma R2 46 | 17 32 399000 91 13.96 Sigma R1 47 | 17 32 340000 89 14.5 Sigma R2 48 | 17 0 358000 85 13.97 Sigma R1 49 | 17 0 393000 91 14.91 Sigma R2 50 | 4 500 516000 83 14.48 NIH R1 51 | 4 500 399000 83 14.85 NIH R2 52 | 4 250 499000 85 14.35 NIH R1 53 | 4 250 457000 79 13.69 NIH R2 54 | 4 125 657000 90 14.02 NIH R1 55 | 4 125 575000 89 13.89 NIH R2 56 | 4 64 405000 81 13.54 NIH R1 57 | 4 64 663000 87 14.37 NIH R2 58 | 4 32 622000 88 14.44 NIH R1 59 | 4 32 528000 83 14.01 NIH R2 60 | 4 0 475000 86 14.57 NIH R1 61 | 4 0 551000 82 13.64 NIH R2 62 | 15 500 305000 73 11.75 NIH R1 63 | 15 500 352000 69 12.9 NIH R2 64 | 15 250 387000 72 13.68 NIH R1 65 | 15 250 369000 72 12.14 NIH R2 66 | 15 125 252000 70 14.86 NIH R1 67 | 15 125 334000 73 13.05 NIH R2 68 | 15 64 235000 71 13.2 NIH R1 69 | 15 64 317000 73 13.13 NIH R2 70 | 15 32 317000 77 13.31 NIH R1 71 | 15 32 305000 68 12.19 NIH R2 72 | 15 0 252000 78 14.3 NIH R1 73 | 15 0 416000 76 12.75 NIH R2 74 | 16 500 452000 88 14.3 NIH R1 75 | 16 500 557000 90 14.88 NIH R2 76 | 16 250 469000 93 15 NIH R1 77 | 16 250 499000 93 14.26 NIH R2 78 | 16 125 499000 93 15.34 NIH R1 79 | 16 125 504000 93 14.74 NIH R2 80 | 16 64 364000 94 15.76 NIH R1 81 | 16 64 446000 94 14.63 NIH R2 82 | 16 32 434000 93 14.3 NIH R1 83 | 16 32 499000 97 14.4 NIH R2 84 | 16 0 405000 90 14.62 NIH R1 85 | 16 0 551000 97 15.36 NIH R2 86 | 17 500 258000 85 14.93 NIH R1 87 | 17 500 499000 89 13.15 NIH R2 88 | 17 250 270000 87 15.35 NIH R1 89 | 17 250 416000 93 14.69 NIH R2 90 | 17 125 217000 80 13.35 NIH R1 91 | 17 125 311000 90 14.28 NIH R2 92 | 17 64 293000 85 15.22 NIH R1 93 | 17 64 346000 89 14.86 NIH R2 94 | 17 32 311000 90 13.7 NIH R1 95 | 17 32 393000 91 12.96 NIH R2 96 | 17 0 311000 88 13.51 NIH R1 97 | 17 0 323000 85 13.33 NIH R2 -------------------------------------------------------------------------------- /analyses/il2-titration/il2-sigma-nih-flow.tsv: -------------------------------------------------------------------------------- 1 | Sample: Donor IL2 Source IL2 concentration (IU/mL) Live/CD4+ CD8+ | Freq. of Parent Live/CD4+ CD8- | Freq. of Parent Live/CD4- CD8+ | Freq. of Parent Live/CD4- CD8- | Freq. of Parent Live/CD25+ | Freq. of Parent Live/CD25- | Freq. of Parent 2 | N4-0.fcs D4 NIH 0 0.96 61.2 34.2 3.57 63 37 3 | N4-32.fcs D4 NIH 32 0.93 63.1 32.4 3.51 61.5 38.5 4 | N4-64.fcs D4 NIH 64 1.29 61.4 33.7 3.54 62.3 37.7 5 | N4-125.fcs D4 NIH 125 0.9 63.7 32.1 3.38 62.1 37.9 6 | N4-250.fcs D4 NIH 250 0.95 63.2 32.5 3.41 62.8 37.2 7 | N4-500.fcs D4 NIH 500 0.74 66.5 29.4 3.41 60 40 8 | N15-0.fcs D15 NIH 0 1.75 83.2 12.1 2.93 57.7 42.3 9 | N15-32.fcs D15 NIH 32 1.67 84 11.2 3.18 59.6 40.4 10 | N15-64.fcs D15 NIH 64 1.76 83.5 11.6 3.19 59.5 40.5 11 | N15-125.fcs D15 NIH 125 1.56 83.2 11.9 3.35 60.4 39.6 12 | N15-250.fcs D15 NIH 250 1.55 83.3 11.7 3.49 60 40 13 | N15-500.fcs D15 NIH 500 1.36 83.2 12.1 3.39 58.2 41.8 14 | N16-0.fcs D16 NIH 0 1.07 61.9 36 1.08 62.9 37.1 15 | N16-32.fcs D16 NIH 32 1.09 61.7 36.1 1.17 61.7 38.3 16 | N16-64.fcs D16 NIH 64 1.13 61.4 36.2 1.26 60.9 39.1 17 | N16-125.fcs D16 NIH 125 1.33 61.8 35.7 1.13 63.2 36.8 18 | N16-250.fcs D16 NIH 250 1.08 61.1 36.7 1.16 60 40 19 | N16-500.fcs D16 NIH 500 1.18 61.6 36 1.17 62 38 20 | N17-0.fcs D17 NIH 0 2.15 55.9 39.5 2.41 70.4 29.6 21 | N17-32.fcs D17 NIH 32 2.52 56.1 38.8 2.6 70 30 22 | N17-64.fcs D17 NIH 64 2.36 56.3 38.8 2.59 69.2 30.8 23 | N17-125.fcs D17 NIH 125 2.59 55 40.2 2.18 68.7 31.3 24 | N17-250.fcs D17 NIH 250 2.76 55.1 39.5 2.61 70.2 29.8 25 | N17-500.fcs D17 NIH 500 2.1 55.5 40 2.41 69.3 30.7 26 | S4-0.fcs D4 Sigma 0 0.74 61.4 34.2 3.71 63.1 36.9 27 | S4-32.fcs D4 Sigma 32 0.61 61.9 33.3 4.17 58.3 41.7 28 | S4-64.fcs D4 Sigma 64 0.62 61.5 33.8 4.04 60.1 39.9 29 | S4-125.fcs D4 Sigma 125 0.68 63.2 32.5 3.67 61.4 38.6 30 | S4-250.fcs D4 Sigma 250 0.67 61.9 33.3 4.19 58.3 41.7 31 | S4-500.fcs D4 Sigma 500 0.44 47.4 22.7 29.4 27.5 72.5 32 | S15-0.fcs D15 Sigma 0 1.12 82.1 13.1 3.66 57.6 42.4 33 | S15-32.fcs D15 Sigma 32 1.22 82.2 12.9 3.65 58.7 41.3 34 | S15-64.fcs D15 Sigma 64 1.29 81.9 12.8 3.97 57.3 42.7 35 | S15-125.fcs D15 Sigma 125 1.21 81.6 13 4.2 57 43 36 | S15-250.fcs D15 Sigma 250 1.19 82.2 12.7 3.98 56.5 43.5 37 | S15-500.fcs D15 Sigma 500 1.17 82.4 12.3 4.12 57.5 42.5 38 | S16-0.fcs D16 Sigma 0 0.75 61.8 36.2 1.24 62.8 37.2 39 | S16-32.fcs D16 Sigma 32 0.85 60.9 36.9 1.31 59.7 40.3 40 | S16-64.fcs D16 Sigma 64 0.86 61.9 36 1.25 59.4 40.6 41 | S16-125.fcs D16 Sigma 125 0.88 61.5 36.4 1.19 60.1 39.9 42 | S16-250.fcs D16 Sigma 250 0.95 61.4 36.4 1.23 61.6 38.4 43 | S16-500.fcs D16 Sigma 500 0.93 61.7 36.1 1.32 62.1 37.9 44 | S17-0.fcs D17 Sigma 0 1.25 55.4 40.2 3.22 66.9 33.1 45 | S17-32.fcs D17 Sigma 32 1.15 55.1 40.6 3.13 66.4 33.6 46 | S17-64.fcs D17 Sigma 64 1.38 56.1 39.4 3.18 69.6 30.4 47 | S17-125.fcs D17 Sigma 125 1.3 55.4 40 3.3 67.5 32.5 48 | S17-250.fcs D17 Sigma 250 1.33 54.6 40.6 3.42 65.6 34.4 49 | S17-500.fcs D17 Sigma 500 1.11 55.2 39.6 4.11 64.1 35.9 50 | -------------------------------------------------------------------------------- /analyses/isolation-bead-titration/Isolation bead titration.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "metadata": {}, 7 | "outputs": [ 8 | { 9 | "name": "stderr", 10 | "output_type": "stream", 11 | "text": [ 12 | "\n", 13 | "Attaching package: ‘dplyr’\n", 14 | "\n", 15 | "The following objects are masked from ‘package:stats’:\n", 16 | "\n", 17 | " filter, lag\n", 18 | "\n", 19 | "The following objects are masked from ‘package:base’:\n", 20 | "\n", 21 | " intersect, setdiff, setequal, union\n", 22 | "\n", 23 | "\n", 24 | "Attaching package: ‘tidyr’\n", 25 | "\n", 26 | "The following object is masked from ‘package:magrittr’:\n", 27 | "\n", 28 | " extract\n", 29 | "\n" 30 | ] 31 | } 32 | ], 33 | "source": [ 34 | "library('readr')\n", 35 | "library('magrittr')\n", 36 | "library('dplyr')\n", 37 | "library('tidyr')\n", 38 | "library('ggplot2')" 39 | ] 40 | }, 41 | { 42 | "cell_type": "code", 43 | "execution_count": 2, 44 | "metadata": {}, 45 | "outputs": [ 46 | { 47 | "data": { 48 | "text/html": [ 49 | "\n", 50 | "\n", 51 | "\n", 52 | "\t\n", 53 | "\t\n", 54 | "\t\n", 55 | "\t\n", 56 | "\t\n", 57 | "\t\n", 58 | "\t\n", 59 | "\t\n", 60 | "\t\n", 61 | "\t\n", 62 | "\t\n", 63 | "\t\n", 64 | "\n", 65 | "
ReplicateBead:cell ratioLive cells/CD3+ | Freq. of Parent (%)Live cells/CD3- | Freq. of Parent (%)Live cells/CD3+/CD3+ CD8- CD4+ | Freq. of Parent (%)Live cells/CD3+/CD3+ CD8+ CD4- | Freq. of Parent (%)
R1 0:1 29.170.937.817.1
R1 1:1 88.711.371.415.8
R1 1:2 81.618.477.217.8
R1 1:4 73.926.176.918.5
R2 0:1 47.552.577.518.3
R2 1:1 89.011.078.716.4
R2 1:2 74.125.978.516.1
R2 1:4 72.527.577.218.6
R3 0:1 48.551.577.318.6
R3 1:1 88.611.479.515.3
R3 1:2 79.920.177.518.4
R3 1:4 72.727.377.218.5
\n" 66 | ], 67 | "text/latex": [ 68 | "\\begin{tabular}{r|llllll}\n", 69 | " Replicate & Bead:cell ratio & Live cells/CD3+ \\textbar{} Freq. of Parent (\\%) & Live cells/CD3- \\textbar{} Freq. of Parent (\\%) & Live cells/CD3+/CD3+ CD8- CD4+ \\textbar{} Freq. of Parent (\\%) & Live cells/CD3+/CD3+ CD8+ CD4- \\textbar{} Freq. of Parent (\\%)\\\\\n", 70 | "\\hline\n", 71 | "\t R1 & 0:1 & 29.1 & 70.9 & 37.8 & 17.1\\\\\n", 72 | "\t R1 & 1:1 & 88.7 & 11.3 & 71.4 & 15.8\\\\\n", 73 | "\t R1 & 1:2 & 81.6 & 18.4 & 77.2 & 17.8\\\\\n", 74 | "\t R1 & 1:4 & 73.9 & 26.1 & 76.9 & 18.5\\\\\n", 75 | "\t R2 & 0:1 & 47.5 & 52.5 & 77.5 & 18.3\\\\\n", 76 | "\t R2 & 1:1 & 89.0 & 11.0 & 78.7 & 16.4\\\\\n", 77 | "\t R2 & 1:2 & 74.1 & 25.9 & 78.5 & 16.1\\\\\n", 78 | "\t R2 & 1:4 & 72.5 & 27.5 & 77.2 & 18.6\\\\\n", 79 | "\t R3 & 0:1 & 48.5 & 51.5 & 77.3 & 18.6\\\\\n", 80 | "\t R3 & 1:1 & 88.6 & 11.4 & 79.5 & 15.3\\\\\n", 81 | "\t R3 & 1:2 & 79.9 & 20.1 & 77.5 & 18.4\\\\\n", 82 | "\t R3 & 1:4 & 72.7 & 27.3 & 77.2 & 18.5\\\\\n", 83 | "\\end{tabular}\n" 84 | ], 85 | "text/markdown": [ 86 | "\n", 87 | "Replicate | Bead:cell ratio | Live cells/CD3+ | Freq. of Parent (%) | Live cells/CD3- | Freq. of Parent (%) | Live cells/CD3+/CD3+ CD8- CD4+ | Freq. of Parent (%) | Live cells/CD3+/CD3+ CD8+ CD4- | Freq. of Parent (%) | \n", 88 | "|---|---|---|---|---|---|---|---|---|---|---|---|\n", 89 | "| R1 | 0:1 | 29.1 | 70.9 | 37.8 | 17.1 | \n", 90 | "| R1 | 1:1 | 88.7 | 11.3 | 71.4 | 15.8 | \n", 91 | "| R1 | 1:2 | 81.6 | 18.4 | 77.2 | 17.8 | \n", 92 | "| R1 | 1:4 | 73.9 | 26.1 | 76.9 | 18.5 | \n", 93 | "| R2 | 0:1 | 47.5 | 52.5 | 77.5 | 18.3 | \n", 94 | "| R2 | 1:1 | 89.0 | 11.0 | 78.7 | 16.4 | \n", 95 | "| R2 | 1:2 | 74.1 | 25.9 | 78.5 | 16.1 | \n", 96 | "| R2 | 1:4 | 72.5 | 27.5 | 77.2 | 18.6 | \n", 97 | "| R3 | 0:1 | 48.5 | 51.5 | 77.3 | 18.6 | \n", 98 | "| R3 | 1:1 | 88.6 | 11.4 | 79.5 | 15.3 | \n", 99 | "| R3 | 1:2 | 79.9 | 20.1 | 77.5 | 18.4 | \n", 100 | "| R3 | 1:4 | 72.7 | 27.3 | 77.2 | 18.5 | \n", 101 | "\n", 102 | "\n" 103 | ], 104 | "text/plain": [ 105 | " Replicate Bead:cell ratio Live cells/CD3+ | Freq. of Parent (%)\n", 106 | "1 R1 0:1 29.1 \n", 107 | "2 R1 1:1 88.7 \n", 108 | "3 R1 1:2 81.6 \n", 109 | "4 R1 1:4 73.9 \n", 110 | "5 R2 0:1 47.5 \n", 111 | "6 R2 1:1 89.0 \n", 112 | "7 R2 1:2 74.1 \n", 113 | "8 R2 1:4 72.5 \n", 114 | "9 R3 0:1 48.5 \n", 115 | "10 R3 1:1 88.6 \n", 116 | "11 R3 1:2 79.9 \n", 117 | "12 R3 1:4 72.7 \n", 118 | " Live cells/CD3- | Freq. of Parent (%)\n", 119 | "1 70.9 \n", 120 | "2 11.3 \n", 121 | "3 18.4 \n", 122 | "4 26.1 \n", 123 | "5 52.5 \n", 124 | "6 11.0 \n", 125 | "7 25.9 \n", 126 | "8 27.5 \n", 127 | "9 51.5 \n", 128 | "10 11.4 \n", 129 | "11 20.1 \n", 130 | "12 27.3 \n", 131 | " Live cells/CD3+/CD3+ CD8- CD4+ | Freq. of Parent (%)\n", 132 | "1 37.8 \n", 133 | "2 71.4 \n", 134 | "3 77.2 \n", 135 | "4 76.9 \n", 136 | "5 77.5 \n", 137 | "6 78.7 \n", 138 | "7 78.5 \n", 139 | "8 77.2 \n", 140 | "9 77.3 \n", 141 | "10 79.5 \n", 142 | "11 77.5 \n", 143 | "12 77.2 \n", 144 | " Live cells/CD3+/CD3+ CD8+ CD4- | Freq. of Parent (%)\n", 145 | "1 17.1 \n", 146 | "2 15.8 \n", 147 | "3 17.8 \n", 148 | "4 18.5 \n", 149 | "5 18.3 \n", 150 | "6 16.4 \n", 151 | "7 16.1 \n", 152 | "8 18.6 \n", 153 | "9 18.6 \n", 154 | "10 15.3 \n", 155 | "11 18.4 \n", 156 | "12 18.5 " 157 | ] 158 | }, 159 | "metadata": {}, 160 | "output_type": "display_data" 161 | } 162 | ], 163 | "source": [ 164 | "cd348_stats <- \n", 165 | " read_tsv(\n", 166 | " './cd3-cd4-cd8-stats.tsv',\n", 167 | " col_types=cols(\n", 168 | " `Replicate`=col_factor(levels=c('R1', 'R2', 'R3')),\n", 169 | " `Bead:cell ratio`=col_factor(levels=c('0:1', '1:1', '1:2', '1:4')),\n", 170 | " .default=col_double()\n", 171 | " )\n", 172 | " )\n", 173 | "cd348_stats" 174 | ] 175 | }, 176 | { 177 | "cell_type": "code", 178 | "execution_count": 3, 179 | "metadata": {}, 180 | "outputs": [ 181 | { 182 | "data": {}, 183 | "metadata": {}, 184 | "output_type": "display_data" 185 | }, 186 | { 187 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V3+/HiNAAIIIIAAAggggAACCKRLIK0BkgrVsmVLW758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bpxiQ4cEHH6Q4gECZB64oY+xljDleQmWM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\naMv3xkB91vt1NlD5w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ceKHHRv94Uh3y\nOlVvvJrtJ2JqNrUac7NtF3ZZq+2PwTCqw6Vn7Y9R8Pqaop3htNZaa/W47qqv8pYTIECAAIH+\nBCRI/elYR4AAAQIECBAgQIBAVwkYpKGrultjCRAgQIAAAQIECBDoT0CC1J+OdQQIECBAgAAB\nAgQIdJWABKmrultjCRAgQIAAAQIECBDoT0CC1J+OdQQIECBAgAABAgQIdJWABKmrultjCRAg\nQIAAAQIECBDoT0CC1J+OdQQIECBAgAABAgQIdJWABKmrultjCRAgQIAAAQIECBDoT+D/AQOJ\nUQ1N1chXAAAAAElFTkSuQmCC", 189 | "text/plain": [ 190 | "plot without title" 191 | ] 192 | }, 193 | "metadata": {}, 194 | "output_type": "display_data" 195 | } 196 | ], 197 | "source": [ 198 | "cd348_grp <- cd348_stats %>% group_by(`Bead:cell ratio`)\n", 199 | "\n", 200 | "rbind(\n", 201 | " cd348_grp %>%\n", 202 | " summarize(\n", 203 | " `Freq_mean`=mean(`Live cells/CD3+ | Freq. of Parent (%)`),\n", 204 | " `Freq_sd`=sd(`Live cells/CD3+ | Freq. of Parent (%)`)\n", 205 | " ) %>%\n", 206 | " mutate(`Population`=\"CD3+\"),\n", 207 | " cd348_grp %>%\n", 208 | " summarize(\n", 209 | " `Freq_mean`=mean(`Live cells/CD3+/CD3+ CD8- CD4+ | Freq. of Parent (%)`),\n", 210 | " `Freq_sd`=sd(`Live cells/CD3+/CD3+ CD8- CD4+ | Freq. of Parent (%)`), \n", 211 | " ) %>%\n", 212 | " mutate(`Population`=\"CD3+ CD4+\"),\n", 213 | " cd348_grp %>%\n", 214 | " summarize(\n", 215 | " `Freq_mean`=mean(`Live cells/CD3+/CD3+ CD8+ CD4- | Freq. of Parent (%)`),\n", 216 | " `Freq_sd`=sd(`Live cells/CD3+/CD3+ CD8+ CD4- | Freq. of Parent (%)`)\n", 217 | " ) %>%\n", 218 | " mutate(`Population`=\"CD3+ CD8+\")\n", 219 | ") %>%\n", 220 | "mutate(`Population`=factor(`Population`)) %>%\n", 221 | "ggplot(aes(x=`Bead:cell ratio`, y=`Freq_mean`, fill=`Bead:cell ratio`)) +\n", 222 | " geom_col() +\n", 223 | " geom_errorbar(\n", 224 | " aes(ymin=`Freq_mean`-`Freq_sd`, ymax=`Freq_mean`+`Freq_sd`),\n", 225 | " width=0.2\n", 226 | " ) +\n", 227 | " facet_wrap(~Population) +\n", 228 | " ylim(0, 100) +\n", 229 | " ylab('Percent population (%)\\n(n=3)')\n" 230 | ] 231 | }, 232 | { 233 | "cell_type": "markdown", 234 | "metadata": {}, 235 | "source": [ 236 | "| Cell count (106 live cells/ml) | 1:1 | 1:2 | 1:4 | 1:8 |\n", 237 | "| ------------------------------ | --- | --- | --- | --- |\n", 238 | "| #1| 3.21 (96%) | 4.16 (93%) | 4.91 (78%) | 5.01 (69%) |\n", 239 | "| #2 | 4.72 (96%) | 3.95 (91%) | 4.81 (75%) | 4.95 (70%) |" 240 | ] 241 | } 242 | ], 243 | "metadata": { 244 | "kernelspec": { 245 | "display_name": "R", 246 | "language": "R", 247 | "name": "ir" 248 | }, 249 | "language_info": { 250 | "codemirror_mode": "r", 251 | "file_extension": ".r", 252 | "mimetype": "text/x-r-source", 253 | "name": "R", 254 | "pygments_lexer": "r", 255 | "version": "3.4.1" 256 | } 257 | }, 258 | "nbformat": 4, 259 | "nbformat_minor": 2 260 | } 261 | -------------------------------------------------------------------------------- /analyses/isolation-bead-titration/cd3-cd4-cd8-stats.tsv: -------------------------------------------------------------------------------- 1 | Replicate Bead:cell ratio Live cells/CD3+ | Freq. of Parent (%) Live cells/CD3- | Freq. of Parent (%) Live cells/CD3+/CD3+ CD8- CD4+ | Freq. of Parent (%) Live cells/CD3+/CD3+ CD8+ CD4- | Freq. of Parent (%) 2 | R1 0:1 29.1 70.9 37.8 17.1 3 | R1 1:1 88.7 11.3 71.4 15.8 4 | R1 1:2 81.6 18.4 77.2 17.8 5 | R1 1:4 73.9 26.1 76.9 18.5 6 | R2 0:1 47.5 52.5 77.5 18.3 7 | R2 1:1 89 11 78.7 16.4 8 | R2 1:2 74.1 25.9 78.5 16.1 9 | R2 1:4 72.5 27.5 77.2 18.6 10 | R3 0:1 48.5 51.5 77.3 18.6 11 | R3 1:1 88.6 11.4 79.5 15.3 12 | R3 1:2 79.9 20.1 77.5 18.4 13 | R3 1:4 72.7 27.3 77.2 18.5 14 | -------------------------------------------------------------------------------- /analyses/mrna-electroporation/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hammerlab/t-cell-guide/3b95f3abebed6e6042b353fb58639729fe8823d3/analyses/mrna-electroporation/.DS_Store -------------------------------------------------------------------------------- /analyses/mrna-electroporation/data.csv: -------------------------------------------------------------------------------- 1 | Donor,Day,Condition,Statistic,Value 2 | Donor 10,1,No RNA,GFP+,1.02 3 | Donor 10,2,No RNA,GFP+,0.47000000000000003 4 | Donor 10,3,No RNA,GFP+,0.3 5 | Donor 10,4,No RNA,GFP+,0.24000000000000002 6 | Donor 10,5,No RNA,GFP+,0.2 7 | Donor 10,6,No RNA,GFP+,0.15000000000000002 8 | Donor 10,1,1600 ng,GFP+,73 9 | Donor 10,2,1600 ng,GFP+,58.7 10 | Donor 10,3,1600 ng,GFP+,48.6 11 | Donor 10,4,1600 ng,GFP+,31.6 12 | Donor 10,5,1600 ng,GFP+,18.4 13 | Donor 10,6,1600 ng,GFP+,11.7 14 | Donor 10,1,800 ng,GFP+,66.3 15 | Donor 10,2,800 ng,GFP+,52.4 16 | Donor 10,3,800 ng,GFP+,42.4 17 | Donor 10,4,800 ng,GFP+,14.7 18 | Donor 10,5,800 ng,GFP+,3.9699999999999998 19 | Donor 10,6,800 ng,GFP+,1.1 20 | Donor 10,1,400 ng,GFP+,47.1 21 | Donor 10,2,400 ng,GFP+,44.4 22 | Donor 10,3,400 ng,GFP+,13.2 23 | Donor 10,4,400 ng,GFP+,2.03 24 | Donor 10,5,400 ng,GFP+,0.6 25 | Donor 10,6,400 ng,GFP+,0.21000000000000002 26 | Donor 12,2,No RNA,GFP+,0.41000000000000003 27 | Donor 12,5,No RNA,GFP+,0.12000000000000001 28 | Donor 12,3,No RNA,GFP+,0.18 29 | Donor 12,2,1600 ng,GFP+,76 30 | Donor 12,3,1600 ng,GFP+,58.1 31 | Donor 12,5,1600 ng,GFP+,33.3 32 | Donor 12,2,800 ng,GFP+,81 33 | Donor 12,3,800 ng,GFP+,64.1 34 | Donor 12,5,800 ng,GFP+,22 35 | Donor 12,2,400 ng,GFP+,70.6 36 | Donor 12,3,400 ng,GFP+,39.3 37 | Donor 12,5,400 ng,GFP+,4.14 38 | Donor 12,4,No RNA,GFP+,0.14 39 | Donor 12,4,1600 ng,GFP+,47.1 40 | Donor 12,4,800 ng,GFP+,43 41 | Donor 12,4,400 ng,GFP+,12.1 42 | Donor 12,1,No RNA,GFP+,2.19 43 | Donor 12,1,1600 ng,GFP+,87.7 44 | Donor 12,1,800 ng,GFP+,88 45 | Donor 12,1,400 ng,GFP+,85.3 46 | Donor 12,6,No RNA,GFP+,0.065 47 | Donor 12,6,1600 ng,GFP+,25 48 | Donor 12,6,800 ng,GFP+,9.39 49 | Donor 12,6,400 ng,GFP+,1.21 50 | Donor 14,1,No RNA,GFP+,0.43 51 | Donor 14,1,1600 ng,GFP+,85.3 52 | Donor 14,1,800 ng,GFP+,24 53 | Donor 14,1,400 ng,GFP+,0.29 54 | Donor 15,1,No RNA,GFP+,1.61 55 | Donor 15,1,1600 ng,GFP+,87.3 56 | Donor 15,1,800 ng,GFP+,51.2 57 | Donor 15,1,400 ng,GFP+,18.2 58 | Donor 14,2,No RNA,GFP+,0.4 59 | Donor 14,2,1600 ng,GFP+,53.4 60 | Donor 14,2,800 ng,GFP+,1.23 61 | Donor 14,2,400 ng,GFP+,0.3 62 | Donor 15,2,No RNA,GFP+,0.41 63 | Donor 15,2,1600 ng,GFP+,72.1 64 | Donor 15,2,800 ng,GFP+,6.6 65 | Donor 15,2,400 ng,GFP+,1.2 66 | Donor 14,3,No RNA,GFP+,0.3 67 | Donor 14,3,1600 ng,GFP+,20.7 68 | Donor 14,3,800 ng,GFP+,0.32 69 | Donor 14,3,400 ng,GFP+,0.23 70 | Donor 15,3,No RNA,GFP+,0.42 71 | Donor 15,3,1600 ng,GFP+,40.2 72 | Donor 15,3,800 ng,GFP+,0.6 73 | Donor 15,3,400 ng,GFP+,0.31 74 | Donor 14,4,No RNA,GFP+,0.1 75 | Donor 14,4,1600 ng,GFP+,2.57 76 | Donor 14,4,800 ng,GFP+,0.087 77 | Donor 14,4,400 ng,GFP+,0.075 78 | Donor 15,4,No RNA,GFP+,0.068 79 | Donor 15,4,1600 ng,GFP+,14.7 80 | Donor 15,4,800 ng,GFP+,0.12 81 | Donor 15,4,400 ng,GFP+,0.077 82 | Donor 14,5,No RNA,GFP+,0.62 83 | Donor 14,5,1600 ng,GFP+,2.25 84 | Donor 14,5,800 ng,GFP+,0.48 85 | Donor 14,5,400 ng,GFP+,0.39 86 | Donor 15,5,No RNA,GFP+,0.54 87 | Donor 15,5,1600 ng,GFP+,10.9 88 | Donor 15,5,800 ng,GFP+,0.65 89 | Donor 15,5,400 ng,GFP+,0.57 90 | Donor 14,6,No RNA,GFP+,0.62 91 | Donor 14,6,1600 ng,GFP+,1.08 92 | Donor 14,6,800 ng,GFP+,0.42 93 | Donor 14,6,400 ng,GFP+,0.49 94 | Donor 15,6,No RNA,GFP+,0.44 95 | Donor 15,6,1600 ng,GFP+,4.17 96 | Donor 15,6,800 ng,GFP+,0.44 97 | Donor 15,6,400 ng,GFP+,0.5 98 | -------------------------------------------------------------------------------- /analyses/mrna-electroporation/donor-difference/act_vs_unac-flow.tsv: -------------------------------------------------------------------------------- 1 | Sample: Live | Freq. of Parent Live/GFP+ | Freq. of Parent Live/GFP- | Freq. of Parent Donor Activated Replicate Electroporation 2 | 16A0-1.fcs 85.9 0.15 99.8 D16 Yes 1 None 3 | 16A0-2.fcs 86.2 0.28 99.7 D16 Yes 2 None 4 | 16A0-3.fcs 85.6 0.25 99.8 D16 Yes 3 None 5 | 16A1-1.fcs 67.7 0.77 99.2 D16 Yes 1 1600V 10ms 3p 6 | 16A1-2.fcs 66.7 1.23 98.8 D16 Yes 2 1600V 10ms 3p 7 | 16A1-3.fcs 66.6 1 99 D16 Yes 3 1600V 10ms 3p 8 | 16A2-1.fcs D17 19.4 80.6 D16 Yes 1 2200V 20ms 1p 9 | 16A2-2.fcs 19.7 10.5 89.5 D16 Yes 2 2200V 20ms 1p 10 | 16A2-3.fcs 19.7 11.3 88.7 D16 Yes 3 2200V 20ms 1p 11 | 17A0-1.fcs 78 0.34 99.7 D17 Yes 1 None 12 | 17A0-2.fcs 78.9 0.43 99.6 D17 Yes 2 None 13 | 17A0-3.fcs 79.8 0.4 99.6 D17 Yes 3 None 14 | 17A1-1.fcs 51.4 8.73 91.3 D17 Yes 1 1600V 10ms 3p 15 | 17A1-2.fcs 48.2 6.69 93.3 D17 Yes 2 1600V 10ms 3p 16 | 17A1-3.fcs 48.8 5.47 94.5 D17 Yes 3 1600V 10ms 3p 17 | 17A2-1.fcs 18.7 9.38 90.6 D17 Yes 1 2200V 20ms 1p 18 | 17A2-2.fcs 18.7 9.8 90.2 D17 Yes 2 2200V 20ms 1p 19 | 17A2-3.fcs 20.9 7.37 92.6 D17 Yes 3 2200V 20ms 1p 20 | 16U0-1.fcs 0.18 50 50 D16 No 1 None 21 | 16U0-2.fcs 75.1 0.65 99.4 D16 No 2 None 22 | 16U0-3.fcs 77.1 0.89 99.1 D16 No 3 None 23 | 16U1-1.fcs 72.9 0.57 99.4 D16 No 1 1600V 10ms 3p 24 | 16U1-2.fcs 71.8 0.7 99.3 D16 No 2 1600V 10ms 3p 25 | 16U1-3.fcs 76.5 1.21 98.8 D16 No 3 1600V 10ms 3p 26 | 16U2-1.fcs 72.4 0.28 99.7 D16 No 1 2200V 20ms 1p 27 | 16U2-2.fcs 70.4 0.31 99.7 D16 No 2 2200V 20ms 1p 28 | 16U2-3.fcs 58.2 0.28 125 D16 No 3 2200V 20ms 1p 29 | 17U0-1.fcs 78.4 0.5 99.5 D17 No 1 None 30 | 17U0-2.fcs 76.3 0.51 99.5 D17 No 2 None 31 | 17U0-3.fcs 76.7 0.74 99.3 D17 No 3 None 32 | 17U1-1.fcs 73.1 15.2 84.8 D17 No 1 1600V 10ms 3p 33 | 17U1-2.fcs 73.8 15.4 84.6 D17 No 2 1600V 10ms 3p 34 | 17U1-3.fcs 73.2 13.1 86.9 D17 No 3 1600V 10ms 3p 35 | 17U2-1.fcs 61.4 3.42 96.6 D17 No 1 2200V 20ms 1p 36 | 17U2-2.fcs 57.8 0.67 99.3 D17 No 2 2200V 20ms 1p 37 | 17U2-3.fcs 56.1 0.48 99.5 D17 No 3 2200V 20ms 1p 38 | -------------------------------------------------------------------------------- /analyses/mrna-electroporation/donor-difference/gfp-titration.tsv: -------------------------------------------------------------------------------- 1 | Sample: Donor Concentration Replicate Activated Live | Freq. of Parent Activated Live/GFP+ | Freq. of Parent Activated Live/GFP- | Freq. of Parent Unactivated live | Freq. of Parent Unactivated live/GFP+ | Freq. of Parent Unactivated live/GFP- | Freq. of Parent 2 | 1801.fcs D18 0 1 0.57 0.7 99.3 85.9 0.9 99.1 3 | 1802.fcs D18 0 2 0.51 2.18 97.8 88.5 0.88 99.1 4 | 1803.fcs D18 0 3 0.39 1.04 99 89 0.77 99.2 5 | 1811.fcs D18 1000 1 0.6 2.34 97.7 91.7 1.4 98.6 6 | 1812.fcs D18 1000 2 0.41 0.48 99.5 92.8 0.98 99 7 | 1813.fcs D18 1000 3 0.62 1.28 98.7 90.5 1.12 98.9 8 | 1821.fcs D18 2000 1 0.6 16.2 83.8 90.5 11.7 88.3 9 | 1822.fcs D18 2000 2 0.67 18.4 81.6 88.9 11.8 88.2 10 | 1823.fcs D18 2000 3 0.54 18.8 81.2 91.6 10.9 89.1 11 | 1841.fcs D18 4000 1 0.54 22.6 77.4 91.6 12.3 87.7 12 | 1842.fcs D18 4000 2 0.66 22.5 77.5 90.9 13.2 86.8 13 | 1843.fcs D18 4000 3 0.74 24.5 75.5 89.3 13.4 86.6 14 | 1901.fcs D19 0 1 0.54 0.93 99.1 89.7 0.49 99.5 15 | 1902.fcs D19 0 2 0.41 0 100 89.4 0.53 99.5 16 | 1903.fcs D19 0 3 0.35 0.57 99.4 89 0.56 99.4 17 | 1911.fcs D19 1000 1 0.44 1.82 98.2 92.4 0.79 99.2 18 | 1912.fcs D19 1000 2 0.36 0.28 99.7 93.5 0.4 99.6 19 | 1913.fcs D19 1000 3 0.38 0.27 99.7 92.3 0.58 99.4 20 | 1921.fcs D19 2000 1 0.4 0 100 93.9 0.45 99.6 21 | 1922.fcs D19 2000 2 0.55 0.55 99.5 90.7 0.5 99.5 22 | 1923.fcs D19 2000 3 0.49 0.82 99.2 91.8 0.49 99.5 23 | 1941.fcs D19 4000 1 0.4 1.73 98.3 91.2 0.96 99 24 | 1942.fcs D19 4000 2 0.39 1.79 98.2 93.1 0.43 99.6 25 | 1943.fcs D19 4000 3 0.29 1.05 98.9 92.3 0.45 99.5 26 | -------------------------------------------------------------------------------- /analyses/mrna-electroporation/donor-difference/unactivated-flow.tsv: -------------------------------------------------------------------------------- 1 | Sample: Electroporation Donor Live/GFP+ | Freq. of Parent Live/GFP- | Freq. of Parent 2 | 40.fcs No D4 0.41 99.6 3 | 41.fcs Yes D4 27.4 72.6 4 | 120.fcs No D12 0.22 99.8 5 | 121.fcs Yes D12 13.4 86.6 6 | 150.fcs No D15 0.76 99.2 7 | 151.fcs Yes D15 1.85 98.1 8 | 160.fcs No D16 0.82 99.2 9 | 161.fcs Yes D16 0.95 99 10 | 170.fcs No D17 0.46 99.5 11 | 171.fcs Yes D17 0.26 99.7 12 | -------------------------------------------------------------------------------- /analyses/mrna-electroporation/donor-difference/unactivated-flow2.tsv: -------------------------------------------------------------------------------- 1 | Sample: Donor Electroporation Live/GFP+ | Freq. of Parent 2 | 40.fcs D4 No 0.99 3 | 41.fcs D4 Yes 8.75 4 | 70.fcs D7 No 0.8 5 | 71.fcs D7 Yes 5.83 6 | 160.fcs D16 No 0.95 7 | 161.fcs D16 Yes 0.74 8 | 170.fcs D17 No 0.74 9 | 171.fcs D17 Yes 0.62 10 | -------------------------------------------------------------------------------- /analyses/pbmc-direct-activation/pbmc-cd3.tsv: -------------------------------------------------------------------------------- 1 | Sample: IL2 Activation beads Live/CD3+ | Freq. of Parent Live/CD3+/CD4+ CD8+ | Freq. of Parent Live/CD3+/CD4+ CD8- | Freq. of Parent Live/CD3+/CD4- CD8+ | Freq. of Parent Live/CD3+/CD4- CD8- | Freq. of Parent Live/CD3- | Freq. of Parent 2 | P001.fcs - - 81.4 13.1 64.4 21.2 1.28 18.6 3 | P002.fcs - - 80.4 9.85 66 22.9 1.32 19.6 4 | P003.fcs - - 82.5 9.21 66.8 22.7 1.4 17.5 5 | P101.fcs 200 U/mL - 74.2 6.87 63.5 27.9 1.96 25.8 6 | P102.fcs 200 U/mL - 72.3 7.72 62.2 28.3 2.06 27.7 7 | P103.fcs 200 U/mL - 72.2 7.47 62.9 28.1 1.97 27.8 8 | P111.fcs 200 U/mL 1:1 91.7 17.5 69.3 12.8 0.99 8.3 9 | P112.fcs 200 U/mL 1:1 92.1 19.6 67.8 12 1.1 7.86 10 | P113.fcs 200 U/mL 1:1 91.5 18.3 69 12.1 1.04 8.54 11 | -------------------------------------------------------------------------------- /analyses/pbmc-direct-activation/pbmc-counts.tsv: -------------------------------------------------------------------------------- 1 | Replicate Count IL2 Activation bead Live cells per ml Live cell fraction 2 | R1 1 - - 8.21E+04 0.45 3 | R1 2 - - 2.93E+04 0.5 4 | R2 1 - - 1.47E+05 0.76 5 | R2 2 - - 1.11E+05 0.95 6 | R3 1 - - 1.35E+05 0.77 7 | R3 2 - - 4.69E+04 0.8 8 | R1 1 200 U/mL - 1.35E+05 0.43 9 | R1 2 200 U/mL - 1.29E+05 0.42 10 | R2 1 200 U/mL - 1.52E+05 0.34 11 | R2 2 200 U/mL - 1.58E+05 0.42 12 | R3 1 200 U/mL - 1.52E+05 0.58 13 | R3 2 200 U/mL - 1.47E+05 0.47 14 | R1 1 200 U/mL 1:1 9.03E+05 0.65 15 | R1 2 200 U/mL 1:1 7.27E+05 0.64 16 | R2 1 200 U/mL 1:1 7.57E+05 0.58 17 | R2 2 200 U/mL 1:1 9.15E+05 0.68 18 | R3 1 200 U/mL 1:1 9.68E+05 0.67 19 | R3 2 200 U/mL 1:1 8.68E+05 0.71 20 | -------------------------------------------------------------------------------- /analyses/plasmid-electroporation/opt_vs_rmpi1640-r_vs_t-day3.csv: -------------------------------------------------------------------------------- 1 | Media,Buffer,Electroporation,Replicate,GFP+ Percent,Live cells per ml 2 | OPTimizer,R,No,1,0.22,1.77E+06 3 | OPTimizer,R,No,2,0.25,1.87E+06 4 | OPTimizer,R,No,3,0.23,1.85E+06 5 | OPTimizer,R,Yes,1,93.3,1.29E+05 6 | OPTimizer,R,Yes,2,92.5,1.11E+05 7 | OPTimizer,R,Yes,3,93.7,8.53E+04 8 | OPTimizer,T,No,1,0.61,2.26E+06 9 | OPTimizer,T,No,2,0.37,1.75E+06 10 | OPTimizer,T,No,3,0.23,1.97E+06 11 | OPTimizer,T,Yes,1,40.7,4.69E+04 12 | OPTimizer,T,Yes,2,26.5,5.57E+04 13 | OPTimizer,T,Yes,3,27,4.70E+04 14 | RPMI1640,R,No,1,0.42,7.16E+05 15 | RPMI1640,R,No,2,0.5,6.04E+05 16 | RPMI1640,R,No,3,0.47,5.04E+05 17 | RPMI1640,R,Yes,1,69,2.67E+05 18 | RPMI1640,R,Yes,2,69.7,2.23E+05 19 | RPMI1640,R,Yes,3,67.8,2.17E+05 20 | RPMI1640,T,No,1,1.1,7.86E+05 21 | RPMI1640,T,No,2,0.71,7.33E+05 22 | RPMI1640,T,No,3,0.59,8.30E+05 23 | RPMI1640,T,Yes,1,64.2,2.82E+05 24 | RPMI1640,T,Yes,2,65.7,2.11E+05 25 | RPMI1640,T,Yes,3,64.2,2.38E+05 26 | -------------------------------------------------------------------------------- /analyses/pre-post-activation-cell-counts/counts.tsv: -------------------------------------------------------------------------------- 1 | Donor Condition Day Count Total volume (ml) Live count per ml Live fraction Total cells 2 | D8 Thawed D1 1 4.5 2.09E+06 0.98 9.41E+06 3 | D8 Thawed D1 2 4.5 2.11E+06 0.98 9.50E+06 4 | D9 Thawed D1 1 4.5 1.71E+06 0.95 7.70E+06 5 | D9 Thawed D1 2 4.5 1.72E+06 0.96 7.74E+06 6 | D10 Thawed D1 1 4.5 7.80E+05 0.94 3.51E+06 7 | D10 Thawed D1 2 4.5 8.56E+05 0.94 3.85E+06 8 | D11 Thawed D1 1 4.5 2.79E+06 0.98 1.26E+07 9 | D11 Thawed D1 2 4.5 2.37E+06 0.96 1.07E+07 10 | D14 Thawed D1 1 4.5 3.16E+06 0.98 1.42E+07 11 | D14 Thawed D1 2 4.5 3.34E+06 0.96 1.50E+07 12 | D15 Thawed D1 1 4.5 2.96E+06 0.95 1.33E+07 13 | D15 Thawed D1 2 4.5 2.97E+06 0.96 1.34E+07 14 | D8 Pre-activation D2 1 4.5 2.35E+06 0.94 1.06E+07 15 | D8 Pre-activation D2 2 4.5 2.33E+06 0.94 1.05E+07 16 | D9 Pre-activation D2 1 4.5 1.83E+06 0.94 8.24E+06 17 | D9 Pre-activation D2 2 4.5 1.81E+06 0.94 8.15E+06 18 | D10 Pre-activation D2 1 4.5 6.10E+05 0.9 2.75E+06 19 | D10 Pre-activation D2 2 4.5 5.92E+05 0.9 2.66E+06 20 | D11 Pre-activation D2 1 4.5 2.55E+06 0.92 1.15E+07 21 | D11 Pre-activation D2 2 4.5 2.09E+06 0.85 9.41E+06 22 | D14 Pre-activation D2 1 4.5 3.00E+06 0.95 1.35E+07 23 | D14 Pre-activation D2 2 4.5 2.95E+06 0.95 1.33E+07 24 | D15 Pre-activation D2 1 4.5 3.16E+06 0.94 1.42E+07 25 | D15 Pre-activation D2 2 4.5 2.50E+06 0.95 1.13E+07 26 | D8 Debeaded D4 1 4.5 2.13E+06 0.96 9.59E+06 27 | D8 Debeaded D4 2 4.5 2.02E+06 0.97 9.09E+06 28 | D9 Debeaded D4 1 4.5 1.26E+06 0.9 5.67E+06 29 | D9 Debeaded D4 2 4.5 1.28E+06 0.91 5.76E+06 30 | D10 Debeaded D4 1 4.5 5.04E+05 0.83 2.27E+06 31 | D10 Debeaded D4 2 4.5 4.52E+05 0.88 2.03E+06 32 | D11 Debeaded D4 1 4.5 2.80E+06 0.9 1.26E+07 33 | D11 Debeaded D4 2 4.5 2.36E+06 0.9 1.06E+07 34 | D14 Debeaded D4 1 4.5 2.57E+06 0.93 1.16E+07 35 | D14 Debeaded D4 2 4.5 2.70E+06 0.96 1.22E+07 36 | D15 Debeaded D4 1 4.5 2.30E+06 0.91 1.04E+07 37 | D15 Debeaded D4 2 4.5 2.37E+06 0.89 1.07E+07 38 | -------------------------------------------------------------------------------- /analyses/resazurin-assay/d7-cell-titration-data.tsv: -------------------------------------------------------------------------------- 1 | Row C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 2 | A 0.135 0.089 0.061 0.045 0.039 0.029 0.026 0.021 0.024 0.017 0.02 0.02 3 | B 0.144 0.102 0.069 0.055 0.041 0.036 0.031 0.027 0.023 0.02 0.023 0.02 4 | C 0.145 0.101 0.069 0.05 0.04 0.034 0.028 0.024 0.022 0.019 0.02 0.02 5 | D 0.147 0.098 0.067 0.054 0.042 0.034 0.029 0.026 0.023 0.021 0.024 0.021 6 | E 0.141 0.095 0.068 0.053 0.041 0.037 0.029 0.031 0.029 0.023 0.023 0.026 7 | F 0.142 0.099 0.062 0.051 0.038 0.032 0.029 0.026 0.021 0.02 0.022 0.02 8 | G 0.134 0.092 0.064 0.051 0.038 0.035 0.03 0.026 0.022 0.021 0.025 0.024 9 | H 0.167 0.112 0.08 0.073 0.068 0.056 0.054 0.053 0.056 0.054 0.048 0.041 10 | -------------------------------------------------------------------------------- /analyses/tsubset-prevalence/cd3-cd4-cd8.tsv: -------------------------------------------------------------------------------- 1 | Sample: Donor Live/CD3+ | Freq. of Parent Live/CD3+/CD4+ CD8+ | Freq. of Parent Live/CD3+/CD4+ CD8- | Freq. of Parent Live/CD3+/CD4- CD8+ | Freq. of Parent Live/CD3+/CD4- CD8- | Freq. of Parent Live/CD3- | Freq. of Parent 2 | D8_CD4.fcs D8 50.8 0.36 71.2 24.5 3.91 49.2 3 | D9_CD4.fcs D9 85.4 1.21 41.1 55.4 2.37 14.6 4 | D10_CD4.fcs D10 60.9 1.25 49.4 41.9 7.43 39.1 5 | D11_CD4.fcs D11 84 1.16 57.4 37.4 4 16 6 | D12_CD4.fcs D12 96.6 0.91 75.3 21.2 2.63 3.37 7 | D15_CD4.fcs D15 85.9 1.23 75.3 18.8 4.67 14.1 8 | -------------------------------------------------------------------------------- /analyses/tsubset-prevalence/naive-eff-central-memory.tsv: -------------------------------------------------------------------------------- 1 | Sample: Donor Live/CCR7+ CD45RO+ | Freq. of Parent Live/CCR7+ CD45RO- | Freq. of Parent Live/CCR7- CD45RO+ | Freq. of Parent Live/CCR7- CD45RO- | Freq. of Parent 2 | D8_CCR7.fcs D8 18.4 57.1 12.2 12.3 3 | D9_CCR7.fcs D9 12.9 22.8 15.9 48.4 4 | D10_CCR7.fcs D10 16.1 48 13.5 22.4 5 | D11_CCR7.fcs D11 24.3 54.4 7.29 14 6 | D12_CCR7.fcs D12 23.1 63.5 8.53 4.87 7 | D15_CCR7.fcs D15 35.6 39.4 12.6 12.4 8 | -------------------------------------------------------------------------------- /conda.env: -------------------------------------------------------------------------------- 1 | channels: 2 | - bioconda 3 | - conda-forge 4 | - defaults 5 | - r 6 | dependencies: 7 | - bioconductor-biobase=2.38.0=r3.4.1_0 8 | - bioconductor-biocgenerics=0.24.0=r3.4.1_0 9 | - bioconductor-edger=3.20.1=r3.4.1_0 10 | - bioconductor-geoquery=2.46.3=r3.4.1_0 11 | - bioconductor-limma=3.34.1=r3.4.1_0 12 | - r-psych=1.7.8=r3.4.1_0 13 | - r-purrr=0.2.2=1 14 | - libedit=3.1.20170329=0 15 | - ncurses=5.9=10 16 | - pcre=8.39=0 17 | - pyzmq=16.0.2=py36_0 18 | - r-assertthat=0.1=r3.4.1_0 19 | - r-base=3.4.1=3 20 | - r-bh=1.65.0_1=r3.4.1_0 21 | - r-bindr=0.1=r3.4.1_0 22 | - r-bindrcpp=0.2=r3.4.1_0 23 | - r-bitops=1.0_6=r3.4.1_0 24 | - r-broom=0.4.2=r3.4.1_0 25 | - r-cellranger=1.1.0=r3.4.1_0 26 | - r-colorspace=1.3_2=r3.4.1_0 27 | - r-crayon=1.3.2=r3.4.1_0 28 | - r-curl=2.4=r3.4.1_0 29 | - r-dbi=0.6_1=r3.4.1_0 30 | - r-dichromat=2.0_0=r3.4.1_0 31 | - r-digest=0.6.12=r3.4.1_0 32 | - r-dplyr=0.7.4=r3.4.1_0 33 | - r-evaluate=0.10.1=r3.4.1_0 34 | - r-forcats=0.2.0=r3.4.1_0 35 | - r-foreign=0.8_67=r3.4.1_0 36 | - r-ggplot2=2.2.1=r3.4.1_0 37 | - r-glue=1.1.1=r3.4.1_0 38 | - r-gtable=0.2.0=r3.4.1_0 39 | - r-hms=0.3=r3.4.1_0 40 | - r-httr=1.2.1=r3.4.1_0 41 | - r-irdisplay=0.4.4=r3.4.1_0 42 | - r-irkernel=0.8.11=r3.4.1_0 43 | - r-jsonlite=1.4=r3.4.1_0 44 | - r-labeling=0.3=r3.4.1_0 45 | - r-lattice=0.20_34=r3.4.1_0 46 | - 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