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.