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

<p>Supplementary data from (Bont&eacute; et al.) which contains Human and Mouse RNA-seq data including :&nbsp;</p> <ul> <li><strong>Raw counts and TPM/FPKM&nbsp;expression matrices of data analyzed&nbsp;</strong>(genes, individual TEs, TE subfamilies) <ul> <li>raw.counts / fpkm.count / tpm.counts&nbsp;rds files</li> </ul> </li> <li><strong>SQuiRE raw output files&nbsp;</strong> <ul> <li>SQuiRE.results&nbsp;rds files</li> </ul> </li> <li><strong>Seurat processed single cell object</strong> (with genes,&nbsp;TEs, Subfamilies) <ul> <li>SC.object rds files</li> </ul> </li> </ul> <p>In details, Mouse and Human data are labelled as follows :</p> <ul> <li><strong>Mouse.SC :</strong> <ul> <li><strong>Type of data</strong> : Single cell RNA-seq data of sorted CD8+ TILs (model&nbsp;B16 melanoma tumors )</li> <li><strong>Label of samples </strong>: Na&iuml;ve like, Early activated, EffectorMemory, Tpex, Tex</li> <li><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).</li> </ul> </li> <li><strong>Mouse.tumor.TILs :</strong> <ul> <li><strong>Type of data</strong> : bulk&nbsp;RNA-seq data of sorted&nbsp;CD8+&nbsp;TILs (model&nbsp;B16 melanoma tumors)</li> <li><strong>Label of samples </strong>: Tumor Slamf6+ or Tumor Tim3+</li> <li><strong>Origin of the data</strong> : B. C. Miller<em>&nbsp;et al.</em>, Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade.&nbsp;<em>Nature Immunology</em>&nbsp;<strong>20</strong>, 326-336 (2019).</li> </ul> </li> <li><strong>Mouse.LCMV.TILs :</strong>&nbsp; <ul> <li><strong>Type of data</strong> : bulk&nbsp;RNA-seq data of sorted&nbsp;CD8+&nbsp;TILs (model LCMV clone 13)</li> <li><strong>Label of samples </strong>: LCMV Slamf6+ or LCMV Tim3+</li> <li><strong>Origin of the data</strong> :&nbsp;B. C. Miller<em>&nbsp;et al.</em>, Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade.&nbsp;<em>Nature Immunology</em>&nbsp;<strong>20</strong>, 326-336 (2019).</li> </ul> </li> <li><strong>Mouse.LCMV_Fli1.TILs :</strong> <ul> <li><strong>Type of data</strong> : bulk&nbsp;RNA-seq data of sorted&nbsp;CD8+&nbsp;TILs &nbsp;(model&nbsp;LCMV clone 13)</li> <li><strong>Label of samples </strong>: WT&nbsp;or Fli1KO</li> <li><strong>Origin of the data</strong> : Z. Chen<em>&nbsp;et al.</em>, In vivo CD8(+) T cell CRISPR screening reveals control by Fli1 in infection and cancer.&nbsp;<em>Cell</em>&nbsp;<strong>184</strong>, 1262-1280 e1222 (2021).</li> </ul> </li> <li><strong>Human.TILs </strong>: <ul> <li><strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (NSCLC tumor tissue )</li> <li><strong>Label of samples </strong>: Tex&nbsp;or Tpex</li> <li><strong>Origin of the data</strong> : Bont&eacute;&nbsp;et al. (ongoing submission)</li> </ul> </li> </ul> <p>&nbsp;</p> <p>Type of features is&nbsp;labeled as follows:</p> <ul> <li><strong>Gene expression</strong> : genes</li> <li><strong>Individual TE expression</strong> : TEs</li> <li><strong>TE subfamiliy&nbsp;expression</strong> : SF</li> </ul> <p>Metadata corresponding to each expression matrix can be found <a href="https://github.com/pebonte/TE_TILs">here</a>.</p> <p>&nbsp;</p>