Pathogenic CD8+ T Cells in HLA-B*27+ Autoimmune Disease

This Zenodo archive contains the processed data for the paper "Refinement of the Pathogenic T Cell Receptor Motif Suggests Type 17 CD8+ T Cells Initiate HLA-B*27-associated Autoimmunity" (Risch et al.)

This archive contains data only, no code. The GitHub code used to generate the analyses in the paper can be found at https://github.com/Paley-Lab/risch_paley_axSpA_AAU_pathogenic_cd8t/.

Data Organization:

single_cell_analysis.tar.gz: Tarball containing the CellRanger scRNA-seq output matrices, CellRanger VDJ filtered output matrices, and final annotated/filtered metadata for the novel single-cell datasets from the paper (YeiH+CD8+ T cells and HLA-B*27+ gut and blood CD8+ T cells). 

mutational_enrich_matrices.tar.gz: Tarball containing the count matrices for the mutational enrichment experiments from Figure 1. See the Supplementary Methods and the code on our GitHub page for the process used to normalize each matrix and generate enrichment ratios for each sample.

tirtlseq.tar.gz: Tarball containing the processed TIRTL-seq data. Single-chain information is given in the files labeled "pseudobulk", while the per-sample predicted paired-chain data is given in the file labeled "all_samples_paired.tsv". 

Each tarball contains a file called sha256sums.tsv which contains the checksums of the files inside. Once you tar -xvf each tarball, you can verify the integrity of your downloaded files by running shasum -a 256 -c sha256sums.tsv within each directory.

complete_diagnoses.xlsx: Diagnoses for each patient in the datasets uploaded here.

The hashtag_oligos files contain the information necessary to demultiplex the hashtags used in the YeiH sorted CD8+ T cell dataset (hashtag_oligos_yeiH_sort.xlsx) and the gut and blood sorted CD8+ T cell dataset (hashtag_oligos_gut_sort.xlsx), respectively. 

Citation:

• Paper: coming soon (DOI TBD)
• Code: https://github.com/Paley-Lab/risch_paley_axSpA_AAU_pathogenic_cd8t/
• This archive: 10.5281/zenodo.21998424