| Antibodies |
| anti-human CD279 (PD-1) Antibody (clone EH12.2H7) |
Biolegend |
Cat#329904 |
| Mouse IgG1, κ Isotype Ctrl Antibody (clone MOPC-21) |
Biolegend |
Cat#400108 |
| anti-human CD3 Antibody (clone UCHT1) |
Biolegend |
Cat#300428 |
| CD103 (Integrin alpha E) Monoclonal Antibody (clone B-Ly7) |
Invitrogen |
Cat#17–1038–42 |
| anti-human CD8 Antibody (clone SK1) |
Biolegend |
Cat#344724 |
| anti-human CD49a Antibody (clone TS2/7) |
Biolegend |
Cat#328318 |
| anti-human CD69 Antibody (clone FN50) |
Biolegend |
Cat#310906 |
| anti-human CD4 Antibody (clone RPA-T4) |
Biolegend |
Cat#300512 |
| anti-human CD45 Antibody (clone HI30) |
Biolegend |
Cat#304029 |
| anti-human CD3 (clone SK7) |
Biolegend |
Cat#344811 |
| anti-human CD3 (clone OKT3) |
Biolegend |
Cat#317317 |
| Mouse Anti-Human HLA-DR (clone L243) |
BD Biosciences |
Cat#335796 |
| anti-human TIM-3 (clone F38–2E2) |
Biolegend |
Cat#345001 |
| anti-human CD45RO (clone UCHL1) |
Biolegend |
Cat#304202 |
| anti-human GrzB (clone GB11), intracellular |
Biolegend |
Cat#515406 |
| anti-human CD127 (clone A019D5) |
Biolegend |
Cat#351346 |
| Human TruStain FcX (Fc Receptor Blocking Solution) |
Biolegend |
Cat#422301 |
|
|
|
| Biological Samples |
| Healthy patient skin samples |
Weill Cornell Medicine, Department of Dermatology |
https://dermatology.weill.cornell.edu/
|
|
Brigham and Women’s Hospital, Department of Dermatology |
https://www.brighamandwomens.org/dermatology
|
| Melanoma TILs samples |
University of Virginia School of Medicine, Division of Surgical Oncology |
https://surgery.virginia.edu/divisions-of-surgery/surgical-oncology-division/
|
|
|
|
| Chemicals, peptides, and recombinant proteins |
| Collagenase 4 |
Worthington Biochemical |
Cat#LS004188
|
| Dispase II |
Roche |
Cat#04942078001 |
| DNase I |
Roche |
Cat#10104159001 |
|
|
|
| Critical commercial assays |
| Fixation/Permeablization Kit |
BD Biosciences |
Cat#554714 |
| Fixable Aqua Dead Cell Stain Kit |
ThermoFisher Scientific |
Cat#L34966
|
|
|
|
| Deposited data |
| Murine TRM microarrays |
(Mackay et al., 2013) |
GEO: GSE47045
|
|
(Wakim et al., 2012) |
GEO: GSE3915
|
| Runx3 T cell RNA-seq |
(Milner et al., 2017) |
GEO: GSE106107
|
| Melanoma TILs single cell RNA-seq |
(Tirosh et al., 2016) |
GEO: GSE72056
|
| ICB treated Melanoma TILs single cell RNA-seq |
(Sade-Feldman et al., 2018) |
GEO: GSE120575
|
| TCGA bulk RNA-seq |
TCGA Research Network |
https://www.cancer.gov/tcga
|
| Anti-PD-1 +/- anti-CTLA-4 metastatic melanoma bulk RNA-seq |
(Liu et al., 2019) |
Supplementary Data 2; https://doi.org/10.1038/s41591-019-0654-5
|
| Murine LCMV Arm + cl 13 T cell microarrays |
(Doering et al., 2012) |
GEO: GSE41867
|
| Murine LCMV Arm T cell microarray |
(Sarkar et al., 2008) |
GEO: GSE10239
|
| Murine SV40-TAG TIL bulk RNA-seq |
(Philip et al., 2017) |
GEO: GSE89307
|
| Murine VACV–SIINFEKL T cell microarray |
(Pan et al., 2017) |
GEO: GSE79805
|
| Human Yellow Fever vaccine T cell microarray |
(Akondy et al., 2017) |
GEO: GSE26347
|
| Human Yellow Fever vaccine T cell bulk RNA-seq |
(Akondy et al., 2017) |
GEO: GSE100745
|
| B16 Dysfunctional CD8+ TILs RNA-seq (murine signatures) |
(Singer et al., 2016) |
https://doi.org/10.1016/j.cell.2016.08.052
|
| SV40-TAG bulk RNA-seq (murine signatures) |
(Scott et al., 2019) |
GEO: GSE126973
|
| LCMV cl 13 RNA-seq (murine signatures) |
(Im et al., 2016) |
GEO: GSE84105
|
|
(Hudson et al., 2019) |
https://doi.org/10.1016/j.immuni.2019.11.002
|
|
(Beltra et al., 2020) |
https://doi.org/10.1016/j.immuni.2020.04.014
|
| Anergy microarray and RNA-seq (murine signatures) |
(Safford et al., 2005) |
https://doi.org/10.1038/ni1193
|
|
(Zha et al., 2006) |
GEO: GSE5960
|
|
(Provine et al., 2016) |
GEO: GSE73001
|
|
(Brignall et al., 2017) |
https://doi.org/10.4049/jimmunol.1602033
|
| Human Kidney, Bladder, Prostate Cancer TILs RNA-seq (human TILs signatures) |
(Jansen et al., 2019) |
GEO: GSE140430
|
| Hepatocellular carcinoma TILs scRNA-seq (human TILs signatures) |
(Zheng et al., 2017) |
https://doi.org/10.1016/j.cell.2017.05.035
|
| Melanoma TILs scRNA-seq (human TILs signatures) |
(Li et al., 2019) |
https://doi.org/10.1016/j.cell.2018.11.043
|
| Code for TILs scoring and survival analysis |
This paper |
https://doi.org/10.5281/zenodo.6419916
|
|
|
|
| Software and algorithms |
| Picard |
Broad Institute |
http://broadinstitute.github.io/picard/
|
| Bowtie2 |
(Langmead et al., 2009) |
http://bowtie-bio.sourceforge.net/index.shtml
|
| RSEM v1.2.3 |
(Li and Dewey, 2011) |
https://github.com/deweylab/RSEM
|
| Seurat v3 |
(Stuart et al., 2019) |
https://satijalab.org/seurat/index.html
|
| Monocle 2 |
(Trapnell et al., 2014; Qiu et al., 2017a; Qiu et al., 2017b) |
http://cole-trapnell-lab.github.io/monocle-release/docs/
|
| Bioconductor-GSVA |
(Hanzelmann et al., 2013) |
https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
|
| nmle |
CRAN |
https://cran.r-project.org/web/packages/nlme/index.html
|
| clusterProfiler |
(Yu et al., 2012) |
https://guangchuangyu.github.io/software/clusterProfiler/
|
| ConsensusPathDB |
(Cavill et al., 2011) |
http://cpdb.molgen.mpg.de/
|
| Survival R package (3.1–8) |
|
https://cran.r-project.org/src/contrib/survival_3.1-8.tar.gz
|
