| Antibodies |
| Anti-CD27 Brilliant Violet 785 |
Biolegend |
Clone O323, cat# 302832, RRID: AB_2562674 |
| Anti-CD11a Brilliant Violet 650 |
BD Biosciences |
Clone HI111, cat# 563934, RRID: AB_2738493 |
| Anti-CD45RA Brilliant Violet 605 |
Biolegend |
Clone HI100, cat# 304134, RRID: AB_2563814 |
| Anti-PD1 Brilliant Violet 421 |
Biolegend |
Clone E12.2.H7, cat # 329920, RRID: AB_10960742 |
| Anti-CCR7 FITC |
BD Biosciences |
Clone 150503, cat# 561271, RRID: AB_10561679 |
| Anti-CD45d PE-Cy7 |
Biolegend |
Clone 9F10, cat# 304314, RRID: AB_10643278 |
| Anti-CD4 PE-Cy5.5 |
Invitrogen |
Clone S3.5, cat# MHCD0418, RRID: AB_10376013 |
| Anti-CD3 PE-Cy5 |
Biolegend |
Clone HIT3a, cat# 300309, RRID: AB_314045 |
| Anti-CD95 PE/Dazzle |
Biolegend |
Clone DX2, cat# 305634, RRID: AB_2564221 |
| Anti-CD39 PE |
Biolegend |
Clone A1, cat# 328208, RRID: AB_940429 |
| Anti-CD8 APC/Fire 750 |
Biolegend |
Clone RPA-T8, cat# 301066, RRID: AB_2629695 |
| Anti-CXCR3 Alexa 647 |
Biolegend |
Clone G0257, cat # 353712, RRID: AB_10962948 |
| Anti-CD25 Brilliant Violet 650 |
Biolegend |
Clone BC96, cat# 302634, RRID: AB_2563807 |
| Anti-CD38 Brilliant Blue 515 |
BD Biosciences |
Clone HIT1, cat# 564498, RRID: AB_2744374 |
| Anti-ICOS PE-Cy7 |
Biolegend |
Clone C398.4D, cat# 313520, RRID: AB_10643411 |
| Anti-CD127 PE/Dazzle |
Biolegend |
Clone A019D5, cat# 351335, RRID: AB_2563636 |
| Anti-CCR7 PE |
Biolegend |
Clone G043H7, cat# 353203, RRID: AB_10916391 |
| Anti-CD3 Alexa 700 |
BD Biosciences |
Clone SP34-2, cat# 557917, RRID: AB_396938 |
| Anti-CXCR5 Alexa 647 |
Biolegend |
Clone J252D4, cat# 356906, RRID: AB_2561815 |
| Anti-CD45RA Brilliant Ultraviolet 395 |
BD Biosciences |
Clone HI100, cat# 740298, RRID: AB_2740037 |
| Anti-CD8 Brilliant Ultraviolet 496 |
BD Biosciences |
Clone RPA-T8, cat# 612942, RRID: AB_2744460 |
| Anti-CD38 Brilliant Ultraviolet 661 |
BD Biosciences |
Clone HIT2, cat# 565069, RRID: AB_2744377 |
| Anti-CD27 Brilliant Ultraviolet 737 |
BD Biosciences |
Clone L128, cat# 612830, RRID: AB_2744350 |
| Anti-CD3 Brilliant Ultraviolet 805 |
BD Biosciences |
Clone UCHT1, cat# 612896, RRID: AB_2739277 |
| Anti-CXCR3 Brilliant Violet 421 |
Biolegend |
Clone G025H7, cat# 353716, RRID: AB_2561448 |
| Anti-CD49d Brilliant Violet 480 |
BD Biosciences |
Clone 9F10, cat# 566134, RRID: AB_2739533 |
| Anti-PD1 Brilliant Violet 605 |
Biolegend |
Clone E12.2.H7, cat# 563245, RRID: AB_2738091 |
| Anti-CD95 Brilliant Violet 650 |
Biolegend |
Clone DX2, cat# 305642, RRID: AB_2632622 |
| Anti-CD39 Brilliant Violet 711 |
Biolegend |
Clone A1, cat# 328228, RRID: AB_2632894 |
| Anti-CD4 Brilliant Violet 750 |
BD Biosciences |
Clone SK3, cat# 566355, RRID: AB_2744426 |
| Anti-CD28 Brilliant Violet 786 |
BD Biosciences |
Clone CD28.2, cat# 740996, RRID: AB_2740619 |
| Anti-CD127 Brilliant Blue 700 |
BD Biosciences |
Clone HIL-7R-M21, cat# 566398, RRID: AB_2744279 |
| Anti-CX3CR1 biotin |
Biolegend |
Clone 2A9-1, cat# 341617, RRID: AB_2616937 |
| Anti-TOX PE |
Miltenyi |
Clone REA473, cat# 130-120-716, RRID: AB_2801780 |
| Anti-EOMES PE-eF610 |
Invitrogen |
Clone WD1928, cat# 61-4877-42, RRID: AB_2574616 |
| Anti-CTLA4 PE-Cy5 |
BD Biosciences |
Clone BNI3, cat# 561717, RRID: AB_10893816 |
| Anti-GZMB PE-Cy5.5 |
Invitrogen |
Clone GB11, cat# GRB18, RRID: AB_2536541 |
| Anti-Tbet PE-Cy7 |
Biolegend |
Clone 4B10, cat# 644824, RRID: AB_2561761 |
| Anti-TCF7 Alexa 647 |
Cell Signaling Technology |
Clone C63D9, cat# 6709S, RRID: AB_2797631 |
| Anti-Ki67 Alexa 700 |
BD Biosciences |
Clone B56, cat# 561277, RRID: AB_10611571 |
| Anti-TIGIT APC/Fire 750 |
Biolegend |
Clone VSTM3, cat# 372708, RRID: AB_2632755 |
| Anti-CD57 biotin |
Biolegend |
Clone HCD57, discontinued, RRID: AB_1083981 |
| Anti-HLA-DR |
Thermo Fischer |
Clone TU36, cat# MHLDR18, RRID: AB_10372966 |
| Streptavidin Brilliant Blue 790 |
BD Biosciences |
Custom build |
| Anti-IFNg Alexa 700 |
Biolegend |
Clone B27, cat# 506516, RRID:AB_961351 |
| Anti-TNF PE-Cy7 |
Biolegend |
Clone MAb11, cat# 502930, RRID:AB_2204079 |
| Anti-IL-2 Brilliant Violet 750 |
BD Biosciences |
Clone MQ1-17H12, cat# 566361, RRID:AB_2739710 |
| Biological Samples |
|
|
| Human PBMCs |
This paper |
Table S1
|
| Melanoma biopsies (single cell suspension) |
This paper |
Table S1
|
| Critical Commercial Assays |
| Takara Pico Input SMARTer Stranded Total RNA-Seq Kit |
Takara |
cat# #634413 |
| Nextera DNA Library Preparation Kit |
Illumina |
cat # FC-121-1031 |
| Deposited Data |
| Raw sequencing data |
This paper |
Deposited in GEO: GSE179613
|
| Experimental Models: Cell Lines |
| HUMAN HEK293T |
ATCC |
CRL-3216 |
| Oligonucleotides |
| CRISPRi guides (Table S4) |
|
|
| Primers for qPCR (Table S5) |
|
|
| Recombinant DNA |
| LRG 2.1T |
Tarumoto et al. 2018
|
Addgene #108098 |
| psPAX2 |
|
Addgene #12260 |
| pED9x |
This study |
Will be available on Addgene upon publication. |
| Software and Algorithms |
| Genome hg19 |
UCSC |
http://hgdownload.cse.ucsc.edu/goldenpath/hg19/
|
| Blacklisted regions |
UCSC |
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed
|
| bowtie2/2.1.0 |
(Langmead and Salzberg 2012) |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| samtools/1.1 |
http://www.htslib.org/doc/#publications
|
http://samtools.sourceforge.net/
|
| picard tools/1.141 |
Broad Institute |
http://broadinstitute.github.io/picard/
|
| MACS2/2.1.1.20160309 |
(Zhang et al. 2008) |
https://github.com/taoliu/MACS/wiki
|
| BEDTools/2.15 |
(Quinlan and Hall 2010) |
https://bedtools.readthedocs.io/en/latest/
|
| FastQC/0.11.2 |
NA |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
| HOMER/4.10.3 |
(Heinz et al. 2010) |
http://homer.ucsd.edu/homer/
|
| IGV/2.4.16 |
Broad Institute |
http://software.broadinstitute.org/software/igv/
|
| STAR/2.5.2a |
(Dobin et al. 2013) |
https://github.com/alexdobin/STAR
|
| PORT/0.8.4-beta |
http://bioinf.itmat.upenn.edu/benchmarking/rnaseq/port/index.php
|
https://github.com/itmat/Normalization
|
| Flowjo/10.5.3 |
Tree Star |
https://www.flowjo.com/
|
| Python/2.7.5 |
Python Software Foundation |
https://www.python.org/
|
| R/3.5.1 |
The R Foundation |
https://www.r-project.org/
|
| Taiji/0.2 |
(Zhang et al. 2019) |
https://taiji-pipeline.github.io/
|
| Metascape |
(Zhou et al. 2019) |
https://metascape.org
|
| scikit-learn/0.21.3 |
(Pedregosa et al. 2011) |
|
| DESeq2/1.22.2 |
(Love, Huber, and Anders 2014) |
Bioconductor |
| umap/0.2.5.0 |
Tomasz Konopka (2020). umap: Uniform Manifold Approximation and Projection. R package version 0.2.5.0. https://CRAN.R-project.org/package=umap
|
CRAN |
| sva/3.30.1 |
(Leek et al. 2012) |
Bioconductor |
| pheatmap/1.0.12 |
Raivo Kolde (2019). pheatmap: Pretty Heatmaps. R package version 1.0.12. https://CRAN.R-project.org/package=pheatmap
|
CRAN |
| Gviz/1.26.5 |
(Hahne and Ivanek 2016) |
Bioconductor |
| slingshot/1.0.0 |
(Street et al. 2018) |
Bioconductor |
| MASS/ 7.3–51.5 |
(Venables 2002) |
CRAN |
| Bedr/1.0.7 |
Syed Haider, Daryl Waggott and Paul C. Boutros (2019). bedr: Genomic Region Processing using Tools Such as ‘BEDTools’, ‘BEDOPS’ and ‘Tabix’. R package version 1.0.7. https://CRAN.R-project.org/package=bedr
|
CRAN |
| relaimpo/ 2.2–3 |
(Grömping 2006) |
CRAN |
| GSEABase/1.44.0 |
Morgan M, Falcon S and Gentleman R. GSEABase: Gene set enrichment data structures and methods. R package version 1.30.2. |
Bioconductor |
| GSVA/1.30.0 |
(Hänzelmann, Castelo, and Guinney 2013) |
Bioconductor |
| SingleCellExperiment/1.4.1 |
Aaron Lun and Davide Risso (2019). SingleCellExperiment: S4 Classes for Single Cell Data. R package version 1.4.1. |
Bioconductor |
| mclust/ 5.4.5 |
(Scrucca L. 2016) |
CRAN |
| tidyverse/1.3.0 |
(Hadley Wickham 2019) |
CRAN |
| reshape2/1.4.3 |
(Wickham 2007) |
CRAN |
| splitstackshape/1.4.8 |
Ananda Mahto (2019). splitstackshape: Stack and Reshape Datasets After Splitting Concatenated Values. R package version 1.4.8. https://CRAN.R-project.org/package=splitstackshape
|
CRAN |
| RColorBrewer/1.1–2 |
Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1–2. https://CRAN.R-project.org/package=RColorBrewer
|
CRAN |
| Rstatix/ 0.5.0 |
Alboukadel Kassambara (2020). rstatix: Pipe-Friendly Framework for Basic Statistical Tests. R package version 0.5.0. https://CRAN.R-project.org/package=rstatix
|
CRAN |
