KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| InVivoMab anti-mouse CD3ε | Bio X Cell | Cat# BE0001-1 |
| InVivomAb anti-mouse CD28 | Bio X Cell | Cat# BE0015-5 |
| InVivomAb anti-mouse TGF-β | Bio X Cell | Cat# BE0057 |
| InVivomAb polyclonal Armenian hamster IgG | Bio X Cell | Cat# BE0091 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant Mouse IL-27 (NS0-expressed) Protein | R&D SYSTEMS | Cat# 2799-ML-010 |
| Recombinant Mouse IL-12 Protein | R&D SYSTEMS | Cat# 419-ML-050 |
| Mouse IL-4, research grade | Miltenyi Biotec | Cat# 130-097-757 |
| Recombinant Mouse IL-1 beta/IL-1F2 Protein | R&D SYSTEMS | Cat# 419-ML-010 |
| Recombinant Mouse IL-6 Protein | R&D SYSTEMS | Cat# 406-ML-025 |
| Recombinant Mouse IL-23 Protein | R&D SYSTEMS | Cat# 1887-ML-010 |
| Human TGF-β1, premium grade | Miltenyi Biotec | Cat# 130-095-067 |
| Liberase TL Research Grade | Sigma | Cat# 5401020001 |
| DNase I | Sigma | Cat# 10104159001 |
| Fixable viability dye eFluor506 | eBioscience | Cat# 65-0866-14 |
| 7AAD | BD Biosciences | Cat# 559925 |
| Digitonin | Promega | Cat# G9441 |
| Critical Commercial Assays | ||
| RNeasy Plus Mini Kit | QIAGEN | Cat# 74134 |
| iScript Reverse Transcription Supermix | Bio-Rad | Cat# 1708841 |
| TaqMan Fast Advanced Master Mix | Thermo Fisher Scientific | Cat# 4444557 |
| PolyJet In Vitro DNA Transfection Reagent | SignaGen Laboratories | Cat# SL100688 |
| Dual-Luciferase® Reporter Assay System | Promega | Cat# E1960 |
| GeneChip Mouse Genome 430 2.0 Array | Affymetrix | Cat# 900497 |
| Nextera® DNA Sample Preparation Kit | Illumina | Cat# FC-121-1030 |
| MinElute Reaction Cleanup kit | QIAgen | Cat# 28204 |
| Chromium Single Cell 3′ Library & Gel Bead Kit v2 | 10x Genomics | Cat# PN-120237 |
| Chromium Single Cell A Chip Kit | 10x Genomics | Cat# PN-1000009 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GEO: GSE159208 |
| Tr1 ATAC-seq (related to Figures 2B and 6B) | Karwacz et al., 2017 | GEO: GSE92993 |
| Atf3 ChIP-seq (related to Figure 2B) | Garber et al., 2012 | GEO: GSE36104 |
| Fosl2 ChIP-seq (related to Figure 2B) | Ciofani et al., 2012 | GEO: GSE40918 |
| Tbx21 ChIP-seq (related to Figure 2B) | Nakayamada et al., 2011 | GEO: GSE33802 |
| Irf8 ChIP-seq (related to Figure 2B) | Xu et al., 2015 | GEO: GSE70712 |
| Experimental Models: Cell Lines | ||
| 293T cells | GenHunter | Cat# Q401 |
| Platinum-E (Plat-E) Retroviral Packaging Cell Line | Cell Biolabs | Cat# RV-101 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX: 000664 |
| BALB/cJ | The Jackson Laboratory | JAX: 000651 |
| Mouse: Foxp3-GFP | Bettelli et al., 2006 | N/A |
| Mouse: 10BiT | Maynard et al., 2007 | N/A |
| Mouse: Prdm1f/f | Shapiro-Shelef et al., 2003 | JAX: 008100 |
| Mouse: Maff/f | Wende et al., 2012 | N/A |
| Mouse: Ahr KO | Schmidt et al., 1996 | JAX: 002831 |
| Mouse: Atf3f/f | Taketani et al., 2012 | N/A |
| Mouse: Batf KO | Schraml et al., 2009 | JAX: 013758 |
| Mouse: Cebpbf/f | Sterneck et al., 2006 | N/A |
| Mouse: Ets1 KO | Muthusamy et al., 1995 | N/A |
| Mouse: Fosl2f/f | Karreth et al., 2004 | N/A |
| Mouse: Hif1af/f | Ryan et al., 2000 | JAX:007561 |
| Mouse: Irf1 KO | Matsuyama et al., 1993 | JAX: 002762 |
| Mouse: Irf4 KO | Klein et al., 2006 | JAX: 009380 |
| Mouse: Irf8f/f | Feng et al., 2011 | JAX:014175 |
| Mouse: Irf9 KO | Gift from Paul J. Utz | RIKEN: RBRC00915 |
| Mouse: Nfil3f/f | Gascoyne et al., 2009 | N/A |
| Mouse: Stat3f/f | Moh et al., 2007 | JAX: 016923 |
| Mouse: Tbx21 KO | Finotto et al., 2002 | JAX: 004648 |
| Mouse: Bhlhe40 KO | Jiang et al., 2008 | JAX: 029732 |
| Mouse: Hlx+/− | Hentsch et al., 1996 | JAX: 008313 |
| Mouse: Stat4 | Kaplan et al., 1996 | JAX: 002826 |
| Mouse: Batf3 KO | Hildner et al., 2008 | JAX: 013755 |
| Mouse: Nfe2l2 KO | Chan et al., 1996 | JAX: 017009 |
| Mouse: Irf7 KO | Gift from Ian Rifkin | N/A |
| Mouse: Id2f/f | Seillet et al., 2013 | N/A |
| Mouse: Fli1+/− | Gift from Maria Trojanowska | N/A |
| Mouse: Cd4-Cre | Lee et al., 2001 | Taconic: 4196 |
| Mouse: Actin-Cre | Lewandoski et al., 1997 | JAX: 033984 |
| Mouse: Lck-Cre | Hennet et al., 1995 | JAX: 003802 |
| Mouse: dLck-Cre | Wang et al., 2001 | JAX: 012837 |
| Recombinant DNA | ||
| pGL4.10[luc2] Vector | Promega | Cat# E665A |
| pGL4.10-Il10 proximal promoter-luc2 | This paper | N/A |
| pGL4.10-Il10 CNS-9-luc2 | This paper | N/A |
| pGL4.10-Il10 HSS+2.98-luc2 | This paper | N/A |
| pGL4.10-Il10 HSS+6.45-luc2 | This paper | N/A |
| MSCV-IRES-GFP | Gift from Tannishtha Reya | Addgene #20672 |
| MSCV-Maf-IRES-GFP | This paper | N/A |
| MSCV-IRES-Thy1.1 | Gift from Philippa Marrack | N/A |
| MSCV-Prdm1-IRES-Thy1.1 | This paper | N/A |
| Software and Algorithms | ||
| GenePattern | Reich et al., 2006 | https://www.genepattern.org/ |
| EDGE | Leek et al., 2006 | https://www.bioconductor.org/ |
| Tophat | Trapnell et al., 2009 | https://github.com/infphilo/tophat |
| RSEM | Li and Dewey, 2011 | http://deweylab.github.io/RSEM/ |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| RStudio | RStudio | https://www.rstudio.com/ |
| ATAC-seq pipeline | Lee et al., 2016 | https://zenodo.org/record/211733 |
| Integrative Genomics Viewer | Robinson et al., 2017 | http://software.broadinstitute.org/software/igv/ |
| R package Seurat v3 | Butler et al., 2018 | https://satijalab.org/seurat/ |
| FlowJo | FlowJo | https://www.flowjo.com |
| Prism | GraphPad | https://www.graphpad.com |