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 : 

• Raw counts and TPM/FPKM expression matrices of data analyzed (genes, individual TEs, TE subfamilies)
  • raw.counts / fpkm.count / tpm.counts rds files
• SQuiRE raw output files 
  • SQuiRE.results rds files
• Seurat processed single cell object (with genes, TEs, Subfamilies)
  • SC.object rds files

In details, Mouse and Human data are labelled as follows :

• Mouse.SC :
  • Type of data : Single cell RNA-seq data of sorted CD8+ TILs (model B16 melanoma tumors )
  • Label of samples : Naïve like, Early activated, EffectorMemory, Tpex, Tex
  • Origin of the data : 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).
• Mouse.tumor.TILs :
  • Type of data : bulk RNA-seq data of sorted CD8+ TILs (model B16 melanoma tumors)
  • Label of samples : Tumor Slamf6+ or Tumor Tim3+
  • Origin of the data : B. C. Miller et al., Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. Nature Immunology 20, 326-336 (2019).
• Mouse.LCMV.TILs : 
  • Type of data : bulk RNA-seq data of sorted CD8+ TILs (model LCMV clone 13)
  • Label of samples : LCMV Slamf6+ or LCMV Tim3+
  • Origin of the data : B. C. Miller et al., Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. Nature Immunology 20, 326-336 (2019).
• Mouse.LCMV_Fli1.TILs :
  • Type of data : bulk RNA-seq data of sorted CD8+ TILs  (model LCMV clone 13)
  • Label of samples : WT or Fli1KO
  • Origin of the data : Z. Chen et al., In vivo CD8(+) T cell CRISPR screening reveals control by Fli1 in infection and cancer. Cell 184, 1262-1280 e1222 (2021).
• Human.TILs :
  • Type of data : bulk RNA-seq data of sorted CD8+ TILs (NSCLC tumor tissue )
  • Label of samples : Tex or Tpex
  • Origin of the data : Bonté et al. (ongoing submission)

Type of features is labeled as follows:

• Gene expression : genes
• Individual TE expression : TEs
• TE subfamiliy expression : SF

Metadata corresponding to each expression matrix can be found here.