KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Brilliant Violet 605™ anti-human CD279 (PD-1) | BioLegend | Cat# 329923; RRID: AB_11124107 |
| APC/Cyanine7 anti-human CD366 (Tim-3) | BioLegend | Cat# 345025; RRID: AB_2565716 |
| Brilliant Violet 605™ anti-human CD197 (CCR7) | BioLegend | Cat# 353223; RRID: AB_11124325 |
| APC/Cyanine7 anti-human CD45RA | BioLegend | Cat# 304127; RRID: AB_10708419 |
| APC anti-human CD39 | BioLegend | Cat# 328209; RRID: AB_1953233 |
| APC/Cyanine7 anti-mouse CD279 (PD-1) | BioLegend | Cat# 135223; RRID: AB_2563522 |
| PerCP/Cyanine5.5 anti-mouse CD366 (Tim-3) | BioLegend | Cat# 119717; RRID: AB_2571934 |
| APC anti-mouse CD62L | BioLegend | Cat# 104411; RRID: AB_313098 |
| PerCP/Cyanine5.5 anti-mouse/human CD44 | BioLegend | Cat# 103032; RRID: AB_2076204 |
| PE anti-human TNF-α | BioLegend | Cat# 502908; RRID: AB_315260 |
| Alexa Fluor® 700 anti-human IFN-γ | BioLegend | Cat# 506515; RRID: AB_961351 |
| APC anti-mouse TNF-α | BioLegend | Cat# 506307; RRID: AB_315429 |
| PE/Cyanine7 anti-mouse IFN-γ | BioLegend | Cat# 505825; RRID: AB_1595591 |
| PE/Cyanine7 anti-human CD3 | BioLegend | Cat# 317333; RRID: AB_2561451 |
| APC/Cyanine7 anti-mouse CD8a | BioLegend | Cat# 100714; RRID: AB_312753 |
| FITC anti-human CD3 | ThermoFisher Scientific | Cat#11-0038-42; RRID: AB_2043831 |
| PE/Cy7 anti-human CD8 | Biolegend | Cat# 344712; RRID: AB_2044007 |
| Alexa Fluor® 700 anti-human CD4 | Biolegend | Cat# 317426; RRID: AB_571942 |
| Mouse Anti-Actin (clone C4) | Millipore | Cat# MAB1501; RRID: AB_2223041 |
| PE/Cyanine7 anti-human CD25 | BioLegend | Cat# 302612; RRID: AB_314282 |
| Rabbit Anti-IgG Donkey Polyclonal Antibody (HRP) | Cytiva | Cat# NA934-1ML; RRID: AB_772206 |
| Normal Rabbit IgG | Cell Signaling Technology | Ca# 2729S; RRID: AB_1031062 |
| Anti-Histone H3 (acetyl K27) | Abcam | Cat# ab4729; RRID: AB_2118291 |
| Rabbit Anti-SMARCA4 (Brg1) (D1Q7F) | Cell Signaling Technology | Cat# 49360S; RRID: AB_2728743 |
| Rabbit Anti-SS18 (D614Z) | Cell Signaling Technology | Cat# 21792S; RRID: AB_2728667 |
| Rabbit Anti-ARID1A (D2A8U) | Cell Signaling Technology | Cat# 12354S; RRID: AB_2637010 |
| Rabbit Anti-PBRM1 (91894) | Cell Signaling Technology | Cat# 91894S; RRID: AB_2800173 |
| Rabbit Anti-HNF1B | Proteintech | Cat# 12533-1-AP; RRID: AB_2116758 |
|
Bacterial and virus strains | ||
| MegaX DH10B electro-competent bacteria | Life Technologies | Cat# C640003 |
|
Biological samples | ||
| Primary Human CD8+ T cells isolated from PBMCs (Donor 1: 24y/o, Female; Donor 2: 35y/o, Male; Donor 5: 24y/o, Male) | StemCell Technologies Inc | Cat# 70027 |
| Primary Human CD8+/CD4+ T cells isolated from PBMCs (Donor 3: 28y/o, Female; Donor 4: 19y/o, Female; Donor 6: 28y/o, Female; Donor7: <30y/o, N/A; Donor8: <30y/o, Male) | New York Blood Center | https://www.nybc.org/ |
| Primary Human CD3+ T cells isolated from PBMCs: (Donor 9: 43y/o, Male; Donor 10: 42y/o, Female) | Indiana University | N/A |
|
Chemicals, peptides, and recombinant proteins | ||
| Zombie Aqua™ Fixable Viability Kit | BioLegend | Cat# 423101 |
| Zombie Violet™ Fixable Viability Kit | BioLegend | Cat# 423113 |
| eBioscience Foxp3/Transcription Factor Staining Buffer Set kit | Life Technologies | Cat# 00-5523-00 |
| BsmBI-v2 | New England Biolabs | Cat# R0739L |
| Anza Esp1 enzyme | Life Technologies | Cat# IVGN0136 |
| T4 DNA ligase | New England Biolabs | Cat# M0202L |
| ATP | New England Biolabs | Cat# PO756S |
| Plasmid safe ATP-dependent DNase | Thermo Fisher Scientific | Cat# NC9046399 |
| TaKaRa Ex Taq DNA Polymerase | Takara Bio | Cat# RR001B |
| Polyethylenimine (PEI) | Thermo Fisher Scientific | Cat# NC1014320; CAS: 9002-98-6 |
| Polybrene | Santa Cruz Biotechnology | Cat# SC-134220; CAS: 28728-55-4 |
| TaKaRa Ex Taq DNA Polymerase | Takara Bio | Cat# RR001B |
| 10mM 2-Mercaptoethanol | Life Technologies | Cat# 21985023; CAS: 60-24-2 |
| T4 PNK | New England Biolabs | Cat# VWR #101228-174 |
| T4 ligase | New England Biolabs | Cat# M0202M |
| SIINKEFL peptide (OVA 257-264) | Invivogen | Cat# vac-sin |
| ACBI1 | SelleckChem | Cat# S9612; CAS: 2375564-55-7 |
| AU-15330 | MedChem Express LLC | Cat #HY-145388; CAS: 2380274-50-8 |
| Cas9-GFP ribonucleoprotein | Integrated DNA Technologies | Cat#10008100 |
| CMP14 | Courtesy of Jun Qi; Papillon et al.90 | N/A |
| FHT-1015 | MedChemExpress® | Cat# HY-144896; CAS: 2368903-18-6 |
| Recombinant Human IL-2 | Peprotech, Inc. | Cat# 200-02-1MG |
| Recombinant Human IL-7 | Peprotech, Inc. | Cat# 200-07-50UG |
| Recombinant Murine IL-2 | Peprotech, Inc. | Cat# 212-12-50UG |
| Recombinant Murine IL-7 | Peprotech, Inc. | Cat# 212-17-50UG |
| Recombinant Murine IFNg | Peprotech, Inc. | Cat# 315-05 |
| APC Annexin V | BioLegend | Cat# 640920 |
|
Critical commercial assays | ||
| QIAquick Gel Extraction Kit | Qiagen | Cat# 28706X4 |
| Phusion High-Fidelity PCR Kit | Life Technologies | Cat# F553S |
| MinElute Reaction Cleanup Kit | Qiagen | Cat# 28204 |
| PureLink™ HiPure Plasmid Filter Maxiprep Kit | Thermo Fisher Scientific | Cat#K21001 |
| QIAamp DNA Mini Kit | Qiagen | Cat# 51304 |
| PureLink™ HiPure Plasmid Filter Maxiprep Kit | Thermo Fisher Scientific | Cat# K21001 |
| RNeasy Plus Mini Kit | Qiagen | Cat# 74136 |
| Nebnext Poly(A) mRNA Magnetic Isolation Module | New England Biolabs | Cat# E7490 |
| NEXTFLEX® Poly(A) Beads 2.0 | Perkin Elmer | Cat# NOVA-512991 |
| Nebnext Ultra II Directional RNA Library Prep Kit | New England Biolabs | Cat# E7760 |
| NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 | Perkin Elmer | Cat# NOVA-5198-01 |
| Qiagen MinElute Reaction clean up kit | Qiagen | Cat# 28206 |
| NextSeq™ 500/550 High output flow cell kit | Illumina | Cat# 20024906 |
| CellTiterGlo | Promega | Cat# G7571 |
|
Deposited data | ||
| Cut&Tag-seq, RNA-seq, and ATAC-seq | This study | GSE212357 |
| scATAC-seq | Sathpathy et al.60 | GSE181062 |
| scATAC-seq | Kourtis et al.22 | GSE181064 |
| Unprocessed blot images | This study | Mendeley data: https://doi.org/10.17632/7msw2d62r6.1 |
|
Experimental models: Organisms/strains | ||
| Mice (C57BL/6J) | The Jackson Laboratory | Jackson strain #000664; RRID: IMSR_JAX:000664 |
| OT-1 mice (C57BL/6-Tg(TcraTcrb)1100Mjb/J) | The Jackson Laboratory | Jackson strain #003831; RRID: IMSR_JAX:003831 |
| Cas9 Mice (Gt(ROSA)26Sortm1.1 (CAG-cas9*,-EGFP)Fezh/J) | The Jackson Laboratory | Jackson strain #024858; RRID: IMSR_JAX:024858 |
| Rag1KO mice B6.129S7-Rag1<tm1Mom>/J | The Jackson Laboratory | Jackson strain #002216; RRID: IMSR_JAX:002216 |
|
Oligonucleotides | ||
| Mouse sgRNAs oligo pool targeting epigenetic genes | Twist Bioscience | https://www.twistbioscience.com/products/oligopools |
| sgROSA (mouse) 5’-AACGGCTCCA CCACGCTCGG-3’ | This study | N/A |
| sgSMARCA4-1 (mouse, sg1553 in library) 5’- ATAATGGCCTACAAGATGT- 3’ | This study | N/A |
| sgSMARCA4-2 (mouse, sg1554 in library) 5’- ATTGCCCGACCACCTGCAGA- 3’ | This study | N/A |
| sgSMARCC1-1 (mouse, sg1563 in library) 5’- TGCCCCAAGAATGTGACACA- 3’ | This study | N/A |
| sgSMARCC1-2 (mouse, sg1564 in library) 5’- TTGGTGACATGCTTCCCAA- 3’ | This study | N/A |
| sgARID1A-1 (mouse, sg1844 in library) 5’- TGCACCACAAGCACCCAGAG- 3’ | This study | N/A |
| sgARID1A-2 (mouse, sg1845 in library) 5’- GTCACTGAGGAAGCGCACCA- 3’ | This study | N/A |
| sgARID1B-1 (mouse, sg1851 in library) 5’- GCTCAGCACCCCGTACCCCG- 3’ | This study | N/A |
| sgARID1B-2 (mouse, sg1853 in library) 5’- CAGCAGAGCAGCCCATACCC- 3’ | This study | N/A |
| sgDPF2-1 (mouse, sg0385 in library) 5’- TCAGCAGATCCAGACACAGG- 3’ | This study | N/A |
| sgDPF2-2 (mouse, sg0386 in library) 5’- AAGGAGTGAGACAGTACATG- 3’ | This study | N/A |
| sgARID2-1 (mouse, sg1854 in library) 5’- GCCGTTTAAGAAGATCCCTG- 3’ | This study | N/A |
| sgARID2-2 (mouse, sg1858 in library) 5’- ACCAGAGTCACTACTTTAGG- 3’ | This study | N/A |
| SMARCA4 sgRNAs cocktail (human) 5’-ACUCCAGACCCACCCCUGGG-3’5’- CCCUAGCCCGGGUCCCUCGC-3’5’- GUCCUGCUGAGGGCGGCCCU-3’ | Synthego | https://www.synthego.com/products/crispr-kits/gene-knockout-kit |
| HNF1B sgRNAs cocktail (human) 5’-AGCCCUCGUCGCCGGACAAG-3’5’- GGCCGAGCCCGACACCAAGC-3’5’- CGGGGUCACCAAGGAGGUGC-3’ | Synthego | https://www.synthego.com/products/crispr-kits/gene-knockout-kit |
|
Recombinant DNA | ||
| pLKO5.sgRNA.EFS.tRFP plasmid | Addgene | Cat #57823; RRID: Addgene_57823 |
| psPAX2 plasmid | Addgene | Cat#12260; RRID: Addgene_12260 |
| pMD2G plasmid | Addgene | Cat#12259; RRID: Addgene_12259 |
| Epigenetic mouse CRISPR library cloned in pLKO5.sgRNA.EFS.tRFP plasmid | This study | N/A |
| Anti-CD19-FMC63scFV-41BB-GFP | This study | N/A |
|
Software and algorithms | ||
| MAGECK | MAGeCKFlute package119 | https://sourceforge.net/p/mageck/wiki/Home/. |
| STAR v2.5.2b | Dobin et al.120 | https://github.com/alexdobin/STAR; RRID: SCR_004463 |
| deepTools v2.5.3 | Ramírez et al.121 | https://deeptools.readthedocs.io/en/develop/; RRID: SCR_016366 |
| Trimmomatic v0.36 | Bolger et al.122 | http://www.usadellab.org/cms/?page=trimmomatic; RRID: SCR_011848 |
| Bowtie2 v2.29 | Langmead and Salzberg.123 | https://bowtie-bio.sourceforge.net/index.shtml; RRID: SCR_016368 |
| Picard v2.8.0 | Picard.124 | https://github.com/broadinstitute/picard; RRID:SCR_006525 |
| SAMtools v 0.1.19 | Li et al.125 | https://samtools.sourceforge.net; RRID: SCR_002105 |
| MACS2 v2.1.1 software | Zhang et al.126 | https://pypi.org/project/MACS2/; RRID: SCR_013291 |
| UCSC utilities | Kuhn et al.127 | https://genome.ucsc.edu/util.html; RRID: SCR_005780 |
| CutRunTools | Zhu et al.128 | https://zenodo.org/record/3374112#.Y22KTy2B3xs |
| edgeR v3.12.1 | Robinson et al.129 | https://bioconductor.org/packages/release/bioc/html/edgeR.html; RRID: SCR_012802 |
| GSEA | Subramanian et al.130 | https://www.gsea-msigdb.org/gsea/index.jsp; RRID: SCR_003199 |
| DESeq2 v1.30.1 | Love et al.131 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html; RRID: SCR_015687 |
| corpcor | Opgen-Rhein and Strimmer132; Schäfer and Strimmer.133 | https://cran.r-project.org/web/packages/corpcor/index.html |
| Bedtools multiIntersectBed and mergeBed functions | Quinlan and Hall134 | https://bedtools.readthedocs.io/en/latest/ |
| ChIPpeakAnno v3.17.0 | Zhu et al.135 | https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html; RRID: SCR_012828 |
| LOLA v1.12.0 | Sheffield and Bock136 | https://bioconductor.org/packages/release/bioc/html/LOLA.html; RRID: SCR_006912 |
| HOMER v4.9 | Heinz et al.137 | http://homer.ucsd.edu/homer/; RRID: SCR_010881 |
| non-redundant archetype consensus motifs | Vierstra et al.138 | https://www.vierstra.org/resources/motif_clustering |
| GLMnet | Friedman et al.139 | https://glmnet.stanford.edu/index.html; RRID: SCR_015505 |
| ChromVAR | Schep et al.140 | https://greenleaflab.github.io/chromVAR/index.html |
|
Other | ||
| Lymphoprep™ | STEMCELL Technologies Inc | Cat# 07811 |
| Pan T Cell Isolation kit, Human | Miltenyi Biotec | Cat# 130-096-535 |
| CD8+ T Cell Isolation Kit, Human | Miltenyi Biotec | Cat# 130-096-495 |
| CD4+ T Cell Isolation Kit, Human | Miltenyi Biotec | Cat# 130-096-533 |
| CD8a+ T Cell Isolation Kit, Mouse | Miltenyi Biotech | Cat #130-104-075 |
| Human T-Activator CD3/CD28 Dynabeads | Thermo Fisher Scientific | Cat# 11132D |
| Mouse T-Activator CD3/CD28 Dynabeads | Thermo Fisher Scientific | Cat# 11453D |
| ACK lysis buffer | Quality Biological Inc | Cat# 118156101C |
| 1X GlutaMAX | Life Technologies | Cat# 35050061 |
| 1X Non-essential Amino Acids | Life Technologies | Cat# 11140050 |
| 1X Sodium Pyruvate | Thermo Fisher Scientific | Cat# MT25000CI |
| Cell Stimulation Cocktail | Affymetrix | Cat# 00-4970-93 |
| Human TruStain FcX™ | Human TruStain FcX™ | Cat# 422302 |
| Ampure beads | Thermo Fisher Scientific | Cat# NC9933872 |
| Concanavalin A | BioMag®Plus | Cat# 86057 |
| CUTANA pAG-Tn5 | Epicycpher | Cat# 15-1117 |
| 4%−12% Bis-Tris polyacrylamide gels | Life Technologies | Cat# NP0336BOX |
| Immobilon PVDF Transfer Membrane | Millipore | Cat# IPVH00010 |
| eBioscience Brefeldin A Solution | Life Technologies | Cat# 00-4506-51 |
| SuperSignal West Femto Maximum Sensitivity Substrate | Life Technologies | Cat# 34095 |