├── LICENSE ├── README.md ├── images ├── STRS.png ├── STRS_DarkMode.png ├── social_media.afdesign ├── social_media.png └── social_media_DarkMode.afdesign ├── manuscripts ├── STRS_Supplement_vFinal.pdf └── STRS_manuscript_bioRxiv_vFinal.pdf ├── pipelines ├── 10x_STARsolo │ ├── README.md │ ├── Snakefile │ ├── config.yaml │ └── resources │ │ └── barcodes_10x │ │ ├── visium-v1.txt │ │ ├── visium-v1_coordinates.txt │ │ ├── visium-v2.txt │ │ └── visium-v2_coordinates.txt ├── 10x_kallisto │ ├── README.md │ ├── Snakefile │ ├── config.yaml │ ├── reo_T1L_antisense2.gtf │ ├── resources │ │ └── barcodes_10x │ │ │ ├── visium-v1.txt │ │ │ ├── visium-v1_coordinates.txt │ │ │ ├── visium-v2.txt │ │ │ └── visium-v2_coordinates.txt │ └── scripts │ │ ├── allign_pap_c2c12_kallisto.sh │ │ ├── bus2mat.py │ │ └── kb.sh ├── README.md ├── SST_kallisto │ ├── README.md │ ├── Snakefile │ └── config.yaml ├── VASAseq_kallisto │ ├── README.md │ ├── Snakefile │ ├── config.yaml │ ├── resources │ │ └── VASAdrop_custom_whitelist.txt │ └── scripts │ │ └── kb.sh ├── bulk_smRNAseq │ ├── Snakefile │ └── config.yaml ├── pipeline.png ├── sample_sheets │ ├── All_STRS-sample_sheet.csv │ ├── Heart_STRS-sample_sheet.csv │ ├── Isakova_smRNA-sample_sheet.csv │ ├── README.md │ ├── STRS_smRNA-sample_sheet.csv │ ├── SkM_Heart_smRNA-sample_sheet.csv │ ├── SkM_STRS-sample_sheet.csv │ └── Subsampled-STRS-sample_sheet.csv └── sp_mirge3 │ ├── README.md │ ├── Snakefile │ └── config.yaml ├── protocols ├── CG000239_VisiumSpatialGeneExpression_UserGuide_RevE_.pdf ├── README.md ├── STRS_protocol.docx ├── STRS_protocol.pdf └── Yeast_PAP_thermoscientific.pdf ├── references ├── README.md ├── reo_T1L.fasta └── reo_T1L_antisense.gtf ├── resources ├── DGEA │ ├── heart_singlecell_markers.csv │ ├── injury_markers_SkM_STRS.csv │ ├── polyA_markers_AllTissues.csv │ └── reovirus_GEX_monocleGAM_heart.csv ├── README.md ├── SupplementalTable1_Reovirus_xGen_probes.csv ├── TargetScan8 │ ├── TargetScan8.0__let-7-5p_miR-98-5p.predicted_targets.txt │ ├── TargetScan8.0__miR-1-3p_206-3p.predicted_targets.txt │ ├── TargetScan8.0__miR-133-3p.predicted_targets.txt │ ├── TargetScan8.0__miR-142-3p.1.predicted_targets.txt │ ├── TargetScan8.0__miR-142b.predicted_targets.txt │ ├── TargetScan8.0__miR-196-5p.predicted_targets.txt │ ├── TargetScan8.0__miR-1a-5p.predicted_targets.txt │ ├── TargetScan8.0__miR-21-5p.predicted_targets.txt │ ├── TargetScan8.0__miR-326-5p_486-3p_6954-5p.predicted_targets.txt │ ├── TargetScan8.0__miR-378a-5p.predicted_targets.txt │ └── TargetScan8.0__miR-574-5p.predicted_targets.txt ├── accession_info │ └── Isakova_smRNA_atlas_SRR_IDs.csv ├── cb_lists │ ├── CTRL-SkM-D2.txt │ ├── CTRL-SkM-D5.txt │ ├── CTRL-SkM-D7.txt │ ├── T1L_D7PI.txt │ ├── mock_D7PI.txt │ ├── yPAP-Pro_Heart-D7T1L.txt │ ├── yPAP-Pro_Heart-mock.txt │ ├── yPAP-Pro_SkM-D0.txt │ ├── yPAP-Pro_SkM-D2.txt │ ├── yPAP-Pro_SkM-D5.txt │ ├── yPAP-Pro_SkM-D7.txt │ ├── yPAP-SUPER_SkM-D0A.txt │ ├── yPAP-SUPER_SkM-D0B.txt │ ├── yPAP-SUPER_SkM-D2.txt │ ├── yPAP-SUPER_SkM-D5A.txt │ ├── yPAP-SUPER_SkM-D5B.txt │ └── yPAP-SUPER_SkM-D7.txt ├── gene_lists │ ├── GENCODEM28_polyA_features.tsv │ ├── GRCm39_GENCODEm28_gene_info_gtf.tsv │ ├── GRCm39_GENCODEm28_transcript_info_gtf.tsv │ ├── biomaRt_GRCm39_v1.csv │ ├── overlap_M28.tsv │ └── reoT1L_info.csv └── metadata_sheets │ ├── SraRunTable_VASA.txt │ ├── VASAdrop_samples.txt │ ├── heart_sc_metadata.csv │ ├── meta_sheet_C2C12nuc.csv │ ├── meta_sheet_ChROseq.csv │ ├── meta_sheet_MM_Heart_scRNAseq.csv │ ├── meta_sheet_VASAdrop.csv │ ├── meta_sheet_smRNA.csv │ └── meta_sheet_visium.csv └── scripts ├── README.md ├── download_scripts └── download_Isakova_smRNA.py ├── figures ├── FigS_STAR_v_kallisto.R ├── FigS_genexgene.R ├── Fig_S_single_nuc_cell_v1.R ├── fig1_v1.R ├── fig2_SkM_v1.R ├── fig2_SkM_v2.R ├── fig3_heart_v1.R ├── figS2_v1.R ├── fig_S_STRS_QC_metrics_v1.R ├── fig_S_biotypes_v1.R ├── fig_S_deconvolution.R ├── fig_S_mirge_v1.R └── 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