Selective control of transposable element expression during T cell exhaustion and anti-PD1 treatment

Supplementary data from (Bonté et al.) which contains Human and Mouse RNA-seq data including : <strong>Raw counts and TPM/FPKM expression matrices of data analyzed </strong>(genes, individual TEs, TE subfamilies) raw.counts / fpkm.count / tpm.counts rds files <strong>SQuiRE raw output files </strong> SQuiRE.results rds files <strong>Seurat processed single cell object</strong> (with genes, TEs, Subfamilies) SC.object rds files In details, Mouse and Human data are labelled as follows : <strong>Mouse.SC :</strong> <strong>Type of data</strong> : Single cell RNA-seq data of sorted CD8+ TILs (model B16 melanoma tumors ) <strong>Label of samples </strong>: Naïve like, Early activated, EffectorMemory, Tpex, Tex <strong>Origin of the data</strong> : S. J. Carmona, I. Siddiqui, M. Bilous, W. Held, D. Gfeller, Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq. Oncoimmunology 9, 1737369 (2020). <strong>Mouse.tumor.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model B16 melanoma tumors) <strong>Label of samples </strong>: Tumor Slamf6+ or Tumor Tim3+ <strong>Origin of the data</strong> : B. C. Miller<em> et al.</em>, Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. <em>Nature Immunology</em> <strong>20</strong>, 326-336 (2019). <strong>Mouse.LCMV.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model LCMV clone 13) <strong>Label of samples </strong>: LCMV Slamf6+ or LCMV Tim3+ <strong>Origin of the data</strong> : B. C. Miller<em> et al.</em>, Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. <em>Nature Immunology</em> <strong>20</strong>, 326-336 (2019). <strong>Mouse.LCMV_Fli1.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model LCMV clone 13) <strong>Label of samples </strong>: WT or Fli1KO <strong>Origin of the data</strong> : Z. Chen<em> et al.</em>, In vivo CD8(+) T cell CRISPR screening reveals control by Fli1 in infection and cancer. <em>Cell</em> <strong>184</strong>, 1262-1280 e1222 (2021). <strong>Human.TILs </strong>: <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (NSCLC tumor tissue ) <strong>Label of samples </strong>: Tex or Tpex <strong>Origin of the data</strong> : Bonté et al. (ongoing submission) Type of features is labeled as follows: <strong>Gene expression</strong> : genes <strong>Individual TE expression</strong> : TEs <strong>TE subfamiliy expression</strong> : SF Metadata corresponding to each expression matrix can be found here.