| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Brilliant Violet (BV) 421 anti-human CD279 (PD-1) | BioLegend | Cat# 329920; RRID: AB_10960742 |
| BV 711 anti-human CD39 | BioLegend | Cat# 328228; RRID: AB_2632894 |
| BV 570 anti-human CD45RO | BioLegend | Cat# 304225; RRID: AB_11126987 |
| BV 650 anti-human CD8a | BioLegend | Cat# 301041; RRID: AB_11125174 |
| BV 785 anti-human CD4 | BioLegend | Cat# 317442; RRID: AB_2563242 |
| BV 570 anti-human CD127 (IL-7Ralpha) | BioLegend | Cat# 351308; RRID: AB_2832685 |
| BV 570 anti-human IFN-gamma | BioLegend | Cat# 502534; RRID: AB_2563880 |
| BV 421 anti-human Perforin | BioLegend | Cat# 353307; RRID: AB_11149688 |
| Allophycocyanin (APC) anti-human Perforin | BioLegend | Cat# 308112; RRID: AB_2252843 |
| Alexa Fluor (AF) 700 anti-human TNF-alpha | BioLegend | Cat# 502928; RRID: AB_2561315 |
| APC/Fire 750 anti-human CD49a | BioLegend | Cat# 328318; RRID: AB_2810495 |
| Phycoerythrin (PE) anti-human CD366 (Tim-3) | BioLegend | Cat# 345006; RRID: AB_2116576 |
| PE/Cyanine 5 anti-human CD62L | BioLegend | Cat# 304808; RRID: AB_314468 |
| Peridinin-Chlorophyll-Protein (PerCP)/Cyanine 5.5 anti-mouse CD45 | BioLegend | Cat# 103132; RRID: AB_893340 |
| Fluorescein (FITC) anti-human CD103 (Integrin alphaE) | BioLegend | Cat# 350204; RRID: AB_10639865 |
| Biotin anti-human CD103 (Integrin alphaE) | BioLegend | Cat# 350220; RRID: AB_2629646 |
| APC-H7 anti-human CD8 | BD Biosciences | Cat# 641409; RRID: AB_1645737 |
| PE-CF594 anti-human CD197 (CCR7) | BD Biosciences | Cat# 562381; RRID: AB_11153301 |
| PE-CF594 anti-human IL-2 | BD Biosciences | Cat# 562384; RRID: AB_11154601 |
| APC-H7 anti-human CD45 | BD Biosciences | Cat# 560274; RRID: AB_1645480 |
| PE anti-human RUNX3 | BD Biosciences | Cat# 564814; RRID: AB_2738969 |
| APC anti-human CD25 | ThermoFisher Scientific | Cat# 17-0259-42; RRID: AB_1582219 |
| PE/Cyanine 5.5 anti-human Granzyme B | ThermoFisher Scientific | Cat# GRB18; RRID: AB_2536541 |
| APC anti-human TOX | Miltenyi Biotec | Cat# 130-118-335; RRID: AB_2751485 |
| PE/Cyanine 7 anti-human CD223 (LAG-3) | eBioscience | Cat# 25-2239-42; RRID: AB_2573430 |
| APC anti-FMC63 CAR19 | ACROBiosytems | Cat# FM3-AY54P1 |
| Biological samples | ||
| Human Healthy Donor PBMC | Human Immunology Core, University of Pennsylvania | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| PE-conjugated Mesothelin Protein | AcroBiosystems | Cat# MSN-HP2H5 |
| PSMA Protein, Human, Recombinant (His Tag), Biotinylated | Sino Biological | Cat# 15877-H07H-B |
| Recombinant Human TGF-beta 1 Protein | R&D Systems | Cat# 240-B-002 |
| Recombinant Human Interleukin-2 (IL-2) Protein | R&D Systems | Cat# 202-IL-050 |
| Human TGF-β1 Recombinant Protein | Cell Signaling Technology | Cat# 75362S |
| D-Luciferin | PerkinElmer | Cat# 122799 |
| TRIzol | ThermoFisher Scientific | Cat# 15596026 |
| Truecut™ Cas9 Protein v2 | ThermoFisher Scientific | Cat# A36498 |
| Matrigel Basement Membrane Matrix | Corning | Cat# 356234 |
| Alt-R® CRISPR-Cas9 tracrRNA | Integrated DNA Technologies | Cat# 1072534 |
| Collagenase Type IV | STEMCELL Technologies | Cat# 07909 |
| DNase I Solution | STEMCELL Technologies | Cat# 07900 |
| 123count eBeads™ | ThermoFisher Scientific | Cat# 01-1234-42 |
| AMPure Beads | Beckman Coulter | Cat# E6116 |
| Dynabeads human T-activator CD3/CD28 | ThermoFisher Scientific | Cat# 11131D |
| Critical commercial assays | ||
| 96-well RTCA E-plates | Agilent | Cat# 300601010 |
| MycoAlert® Mycoplasma Detection Kit | Lonza | Cat# LT07-318 |
| Pan T cell Isolation Kit, human | Miltenyi Biotec | Cat# 130-096-535 |
| RNA Clean & Concentrator™ Kits | Zymo Research | Cat# R1015 |
| P3 Primary Cell 4D-nucleofector Kit | Lonza | Cat# V4XP-3032 |
| 13-plex LEGENDplex™ Human CD8 Panel | BioLegend | Cat# 740267 |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit | ThermoFisher Scientific | Cat# L34957 |
| Foxp3 Transcription Factor Staining Buffer Set | ThermoFisher Scientific | Cat# 00-5523-00 |
| Chromium Next GEM Single Cell 5′ Kit v2 | 10X Genomics | Cat# PN-1000263 |
| Dead Cell Removal Kit | Miltenyi Biotec | Cat# 130-090-101 |
| Deposited data | ||
| RNA- and ATAC-seq data | NCBI Gene expression omnibus (GEO) | GSE224866 |
| Experimental models: Cell lines | ||
| NALM6, clone G5 | ATCC | CRL-3273 |
| Capan-2 | ATCC | HTB-80 |
| AsPC-1 | ATCC | CRL-1682 |
| PC3 | ATCC | CRL-1435 |
| HEK 293T | ATCC | CRL-3216 |
| EMMESO | Steven M. Albelda Lab | N/A |
| Experimental models: Organisms/strains | ||
| NOD/SCID/IL-2Rγ-null (NSG) mice | University of Pennsylvania Stem Cell and Xenograft Core | N/A |
| Oligonucleotides | ||
| Please see Table S3. | This study | N/A |
| Recombinant DNA | ||
| pTRPE-RUNX3 | Steven M. Albelda Lab | N/A |
| pTRPE-M5 (anti-mesothelin) CAR (4-1BB/CD3ζ) | Carl H. June Lab | N/A |
| pTRPE-SS1 (anti-mesothelin) CAR (4-1BB/CD3ζ) | Carl H. June Lab | N/A |
| pTRPE-PSMA CAR (4-1BB/CD3ζ) | Carl H. June Lab | N/A |
| pTRPE-CD19 CAR (4-1BB/CD3ζ) | Carl H. June Lab | N/A |
| Software and algorithms | ||
| FlowJo v10 | FlowJo, LLC | https://www.flowjo.com; RRID:SCR_008520 |
| GraphPad Prism v9.1.0 | GraphPad | https://www.graphpad.com; RRID:SCR_002798 |
| RTCA 2.0 | Agilent | https://www.agilent.com |
| Inference of CRISPR Edits (ICE) Tool | Synthego | https://ice.synthego.com |
| Cell Ranger v6.1.2 | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct |
| Seurat v4.1.1 | Satija Lab | https://github.com/satijalab/seurat |
| SCTransform (part of Seurat) | Christoph Hafemeister, Rahul Satija | https://github.com/ChristophH/sctransform |
| Functions within Seurat (SelectIntegrationFeatures, PrepSCTIntegration, FindIntegrationAnchors, IntegrateData, RunPCA, FindNeighbors, FindClusters, runUMAP, FindMarkers, FindAllMarkers, AddModuleScore) | Satija Lab | https://satijalab.org/seurat/reference/index.html |
| Cutadapt | Marcel Martin | https://github.com/marcelm/cutadapt |
| Bowtie2 | Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg | https://github.com/BenLangmead/bowtie2 |
| removeChrom | John M. Gaspar | https://github.com/jsh58/harvard/blob/master/removeChrom.py |
| Samtools | Heng Li, Bob Handsaker, and colleagues | https://github.com/samtools/samtools |
| The Integrative Genome Viewer (IGV) | Broad Institute | https://github.com/igvteam/igv |
| MACS2 | Tao Liu and colleagues | https://github.com/taoliu/MACS |
| ENCODE blacklisted regions | Anshul Kundaje Lab | https://sites.google.com/site/anshulkundaje/projects/blacklists |
| findMotifsGenome script from HOMER | Chris Benner and colleagues | http://homer.ucsd.edu/homer/ngs/peakMotifs.html |
| edgeR v3.34.0 | Gordon Smyth, Yunshun Chen, Matthew Ritchie, and colleagues | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| enrichr | Ma’ayan Lab | https://maayanlab.cloud/Enrichr |
| GSEABase | Martin Morgan, Dan Tenenbaum, and colleagues | https://github.com/Bioconductor/GSEABase |
| kallisto v0.46.0 | Páll Melsted, Lior Pachter, and colleagues | https://github.com/pachterlab/kallisto |
| tximport 1.24.0 | Michael Love, Charlotte Soneson, Mark Robinson, and colleagues | https://github.com/mikelove/tximport |
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