Virus:Article Title: Loss of p53 exacerbates autoimmunity by reprogramming propionyl-CoA metabolism and histone modifications in Treg cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Anti-CD152-APC Biolegend Cat# 106310; RRID: AB_2087653 Mouse Anti-CD95 (Fas)-PE Biolegend Cat# 152608; RRID: AB_2632902 Mouse Anti-CD279 (PD-1)-PE Biolegend Cat# 135210; RRID: AB_2159183 Mouse Anti-CD185 (CXCR5)-PE Biolegend Cat# 145504; RRID: AB_2561967 Mouse/Human Anti-GL7Antigen-Pacific Blue Biolegend Cat# 144614; RRID: AB_2563291 Mouse anti-CD45.1-APC Biolegend Cat# 110714; RRID: AB_313503 Human Anti-CD4-Pacific Blue Biolegend Cat# 317424; RRID: AB_571953 Human Anti-CD8a-FITC Biolegend Cat# 301060; RRID: AB_2562055 Human Anti-IL-17A-PE Biolegend Cat# 512305; RRID: AB_961394 Human Anti-IFN-γ-APC Biolegend Cat# 512305; RRID: AB_961394 Human Anti-KLRG1-APC Biolegend Cat# 368605; RRID: AB_2571925 Human Anti-ICOS-FITC Biolegend Cat# 313506; RRID: AB_416329 Human CD3/CD28 T cell Activator STEMCELL Technologies Cat# 10971; RRID: AB_2827806 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXcell Cat# BE0012; RRID: AB_1107619 Bacterial and virus strains DH5α Thermo Fisher Scientific 18265017 Biological samples Healthy people peripheral blood mononuclear cells Tsinghua University N/A Ankylosing spondylitis people peripheral blood mononuclear cells West China Hospital N/A Systemic lupus erythematosus people peripheral blood mononuclear cells West China Hospital N/A Chemicals, peptides, and recombinant proteins RPMI 1640 medium Macgene CM10041 DMEM medium Macgene CM10013 HBSS, without calcium and magnesium Macgene CC016 10×HBSS, without calcium and magnesium Macgene CC016.1 Penicillin-Streptomycin Macgene CC004 Trypsin-EDTA (0.25%), phenol red Macgene CC017 Human TGF-β1 R&D 240-B; GenPept: P01137 Trizol Thermo Scientific 15596 Lipofectamine 2000 Transfection Reagent Thermo Scientific 11668027 FBS Gemini 900–108 Sodium Propionate Sigma-Aldrich P1880 Sodium Succinate Sigma-Aldrich S9637 Sodium Acetate Sigma-Aldrich S5636 anti-FLAG M2 affinity gel Sigma-Aldrich A2220 Polybrene Sigma-Aldrich AL-118 2-Mercaptoethanol Sigma-Aldrich M3148 Brefeldin A Solution Invitrogen 00-4506-51 Monensin Solution Invitrogen 00-4505-51 DAPI Invitrogen D3571 Recombinant Mouse IL-2 Novoprotein CK24 Recombinant Human IL-2 Novoprotein C013 Phosphate-Buffered Saline, without calcium and magnesium Corning 21-040-CV rProtein G MagBeads Yeasen 36419ES03 (Continued on next page) 18 Cell Reports 45, 117084, March 24, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dextran Sulfate Sodium Salt Yeasen 60316ES60 Hieff Trans® Polyethylenimine Linear (PEI) Yeasen 40816ES02 EDTA-free protease inhibitor cocktail Yeasen 20124ES10 FX1 MedChemExpress HY-102027 APG-115 MedChemExpress HY-101518 nutlin-3 MedChemExpress HY-50696 Pifithrin-α hydrobromide MedChemExpress HY-15484 A-485 MedChemExpress HY-107455 Critical commercial assays KOD OneTM PCR Master Mix TOYOBO KMM-101 ReverTra Ace qPCR RT Master Mix with gDNA Remover TOYOBO FSQ-301 Zombie YellowTM Fixable Viability Kit Biolegend 423104 Percoll GE Healthcare 17089101 Ficoll-Paque PLUS GE Healthcare 17144002 Fixation/Permeabilization Diluent Invitrogen 00-5223-56 Fixation/Permeabilization Concentrate Invitrogen 00-5123-43 2×HieffTM PCR Master Mix (With Dye) Yeasen 10102ES08 NovoStart® SYBR qPCR SuperMix Plus Novoprotein E096-01A Mouse IL-6 ELISA Kit CUSABIO CSB-E04639m Mouse IgE ELISA Kit CUSABIO CSB-E07983m Mouse TNF-α ELISA Kit CUSABIO CSB-E04741m Mouse MCP-1/MCAF ELISA Kit CUSABIO CSB-E07430m Dual-Luciferase® Reporter Assay System Promega E1910 EasySepTM Mouse CD4+ T cell Isolation Kit STEMCELL Technologies 19852 EasySepTM Mouse CD25 Regulatory T cell Positive Selection Kit STEMCELL Technologies 18782 EasySepTM Human CD4+CD127lowCD25+ Regulatory T cell Isolation Kit STEMCELL Technologies 18063 EasySepTM Mouse Biotin Positive Selection kit STEMCELL Technologies 17665 Deposited data Metabolomics data This paper MetaboLights: MTBLS13473 Mass spectrometry-based proteomic data This paper iProX: PXD071798 RNA sequencing data This paper GSA: CRA035222 CUT-Tag sequencing data This paper GSA: CRA037882 Raw Western Blots on Mendeley This paper Mendeley Data; https://doi.org/10.17632/ tk3cn3rhb8.4 Experimental models: Cell lines HEK293T ATCC Cat#CRL-3216; RRID: CVCL_0063 MEF This paper N/A Experimental models: Organisms/strains C57BL/6 mice Animal facility at Tsinghua University N/A Cd4Cre mice This study N/A Foxp3Cre mice This study N/A Aldh6a1flox/folx mice Shanghai Model Organism NM-CKO-234466 Trp53flox/flox mice This study N/A Rag1− /− mice This study N/A (Continued on next page) Cell Reports 45, 117084, March 24, 2026 19
Article Title: Regulatory T cell-derived TGF-β signaling governs the differentiation and maintenance of tumor-infiltrating bystander CD8 + T cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PerCP/Cyanine5.5 anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100734; RRID: AB_2075238 Brilliant Violet 510TM anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100752; RRID: AB_2563057 PE anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100707; RRID: AB_312746 PerCP/Cyanine5.5 anti-mouse CD44 (clone IM7) Biolegend Cat# 103032; RRID: AB_ 2076204 APC anti-mouse CD45.1 (clone A20) Biolegend Cat# 110713; RRID: AB_ 313502 Alexa Fluor® 700 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110724; RRID: AB_493733 PE/Cyanine7 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110729; RRID: AB_1134170 PE/Cyanine7 anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104418; RRID: AB_313103 Brilliant Violet 605TM anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104437; RRID: AB_11125577 Brilliant Violet 421TM anti-mouse CD127 (IL-7Rα) (clone A7R34) Biolegend Cat# 135027; RRID: AB_2563103 PE anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 164203; RRID: AB_2936560 FITC anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 104505; RRID: AB_313108 PerCP anti-mouse CD45.1 (clone A20) Biolegend Cat# 110725; RRID: AB_893347 Brilliant Violet 510TM anti-mouse CX3CR1 (clone SA011F11) Biolegend Cat# 149013; RRID: AB_2565697 APC anti-mouse Blimp-1 (clone 5E7) Biolegend Cat# 150007; RRID: AB_2728186 PE anti-mouse/human KLRG1 (MAFA) (clone 2F1) Biolegend Cat# 138407; RRID: AB_10574005 Alexa Fluor® 700 anti-mouse CD45.2 (clone 104) Biolegend Cat# 109822; RRID: AB_493731 Pacific BlueTM anti-mouse CD45.2 (clone 104) Biolegend Cat# 109819; RRID: AB_492873 Alexa Fluor® 700 anti-mouse FOXP3 (clone MF-14) Biolegend Cat# 126421; RRID: AB_2750492 FITC anti-mouse CD25 (clone 3C7) Biolegend Cat# 101907; RRID: AB_961210 PE anti-mouse CD103 (clone W19396D) Biolegend Cat# 110903; RRID: AB_2927994 PE/Cyanine7 anti-mouse CD186 (CXCR6) (clone SA051D1) Biolegend Cat# 151118; RRID: AB_2721669 PerCP/Cyanine5.5 anti-mouse CD49a (clone HMα) Biolegend Cat# 142611; RRID: AB_2750218 TCF1/TCF7 Rabbit mAb (clone C63D9) Cell Signaling Technology Cat# 2203; RRID: N/A (Continued on next page) Cell Reports 45, 117189, April 28, 2026 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER KLF2 Rabbit mAb (clone E2Z1H) Cell Signaling Technology Cat# 15306; RRID: N/A Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM 647 Thermofisher Cat# A-21245; RRID: AB_2535813 Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM Plus 488 Thermofisher Cat# A-32731TR; RRID: AB_2866491 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXCell Cat# BE0012; RRID: AB_1107619 T-Select H-2Db LCMV gp33 (C9M) Tetramer-KAVYNFATM-APC MBL Cat# TS-M512-2 T-Select H-2Db LCMV NP396 Tetramer-FQPQNGQFI-APC MBL Cat# TS-M513-2 H-2Db LCMV gp276-286 Tetramer-SGVENPGGYCL-APC MBL Cat# TS-5009-2 FITC anti-human CD45RA (clone HI100) Biolegend Cat# 304105; RRID: AB_314409 PerCP anti-human CD197 (CCR7) (clone G043H7) Biolegend Cat# 353241; RRID: AB_2564545 PE/Cyanine7 anti-human CD62L (clone S21001C) Biolegend Cat# 385109; RRID: AB_3683426 Alexa Fluor® 700 anti-human CD3 (clone OKT3) Biolegend Cat# 317339; RRID: AB_2563407 Brilliant Violet 605TM anti-human CD69 (clone FN50) Biolegend Cat# 310937; RRID: AB_2562306 Brilliant Violet 711TM anti-human CD8 (clone SK1) Biolegend Cat# 344733; RRID: AB_2565242 PE labeled Pro5 MHC Pentamers A*11:01 SIIPSGPLK PROIMMUNE Cat# 1513 Bacterial and virus strains LCMV Armstrong Dr. Rafi Ahmed N/A Listeria monocytogenes expressing ovalbumin (OVA) This lab N/A Biological samples Human CRC tumor specimens Xinqiao Hospital (Army Medical University) N/A Chemicals, peptides, and recombinant proteins Trypsin-EDTA (0.25%), phenol red Gibco Cat# 25200056 Fetal Bovine Serum (FBS) Gibco Cat# A5669701 RPMI 1640 Gibco Cat# 11875093 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 11965092 L-Glutamine 200mM (100×) Gibco Cat# 25030081 Non-Essential Amino Acids (MEM NEAA) (100×) Gibco Cat# 11140050 Sodium Pyruvate (100mM) Gibco Cat# 11360070 Dimethyl sulfoxide (DMSO) Sigma Cat# 20688 Diphtheria toxin Sigma Cat# D0564 Penicillin-Streptomycin-Glutamine Solution Gibco Cat# 10378016 β-Mercaptoethanol Procell Cat# PB180633 Percoll GE Healthcare Cat# 17-0891-09 FTY720 Merck Cat# SML0700 Peptide: KAVYNFATM (GP33-41) GL Biochem (Shanghai) Ltd Cat# 057477 Human Recombinant IL-2 Novoprotein Cat# C013 Polybrene Sigma-Aldrich Cat# TR-1003 (Continued on next page) 20 Cell Reports 45, 117189, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Gibco Cat# 31985070 TransIT-293 Mirus Cat# MIR 2706 Ficoll TBD Cat# LTS107701 collagenase I Diamond Cat# A004194 collagenase II Diamond Cat# A004174 LY2109761 MedChemExpress Cat# HY-12075 AgeI New England Biolabs Cat# R0552 EcoRI New England Biolabs Cat# R3101 T4 DNA Ligase New England Biolabs Cat# M0202 E. coli DH5α TransGen Cat# CD201 Critical commercial assays LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit Thermofisher Cat# L34975 Cytofix/Cytoperm Fixation/Permeabilization Kit BD Biosciences Cat# 554714; RRID: AB_2869008 FastPure Cell/Tissue Total RNA Isolation Kit V2 Vazyme Cat# RC112-01 RevertAid H Minus First Strand cDNA Synthesis Kit Thermofisher Cat# K1622 AceQ qPCR SYBR Green Master Mix Vazyme Cat# Q111 QIAprep Spin Miniprep Kit-Plasmid purification Qiagen Cat# 270106 MycAway® Mycoplasma Real-time qPCR Detection Kit Yeasen Cat# 40619ES25 Hyperactive ATAC-seq Library Prep Kit for Illumina Vazyme Cat# TD711 Deposited data Raw ATAC-seq data (TCM, TEM, and TRM subsets of TME-infiltrating P14 TBYS cells) This paper GEO: GSE306797 scRNA-seq data of P14 TBYS cells from MC38 TME Chen et al. 10 GEO: GSE222002 scRNA-seq data of P14 TMEM from lymphoid tissue Crowl et al. 24 GEO: GSE182276 scRNA-seq data of P14 TMEM from non-lymphoid tissue Kurd et al.25 GEO: GSE131847 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human CRC Chen et al.27 GEO: GSE236581 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human NSCLC Caushi et al.28 GEO: GSE173351 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human BCC Yost et al.40 GEO: GSE123813 ATAC-seq data of splenic naive P14 CD8+ T cells McDonald et al.32 GEO: GSE228381 ATAC-seq data of splenic P14 TCM and TEM cells Zhao et al. 33 GEO: GSE213041 ATAC-seq data of P14 TRM cell Crowl et al. 24 GEO: GSE182276 Experimental models: Cell lines B16F10 cells ATCC Cat# CRL-6475 MC38 cells Shanghai Model Organisms Center Cat# NM-S13 LLC cells ATCC Cat# CRL-1642 HEK293T cells ATCC Cat# CRL-3216 Experimental models: Organisms/strains Mouse: C57BL/6J (CD45.2) Jackson Laboratory Stock No: 000664 Mouse: C57BL/6-Tg (TcraTcrb) 1100Mjb/J (OT-1) Jackson Laboratory Stock No: 003831 Mouse: B6.Cg-Tcratm1Mom Tg (TcrLCMV) 327Sdz/TacMmjax (P14) From Dr. Rafi.
Recombinant:Article Title: Loss of p53 exacerbates autoimmunity by reprogramming propionyl-CoA metabolism and histone modifications in Treg cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Anti-CD152-APC Biolegend Cat# 106310; RRID: AB_2087653 Mouse Anti-CD95 (Fas)-PE Biolegend Cat# 152608; RRID: AB_2632902 Mouse Anti-CD279 (PD-1)-PE Biolegend Cat# 135210; RRID: AB_2159183 Mouse Anti-CD185 (CXCR5)-PE Biolegend Cat# 145504; RRID: AB_2561967 Mouse/Human Anti-GL7Antigen-Pacific Blue Biolegend Cat# 144614; RRID: AB_2563291 Mouse anti-CD45.1-APC Biolegend Cat# 110714; RRID: AB_313503 Human Anti-CD4-Pacific Blue Biolegend Cat# 317424; RRID: AB_571953 Human Anti-CD8a-FITC Biolegend Cat# 301060; RRID: AB_2562055 Human Anti-IL-17A-PE Biolegend Cat# 512305; RRID: AB_961394 Human Anti-IFN-γ-APC Biolegend Cat# 512305; RRID: AB_961394 Human Anti-KLRG1-APC Biolegend Cat# 368605; RRID: AB_2571925 Human Anti-ICOS-FITC Biolegend Cat# 313506; RRID: AB_416329 Human CD3/CD28 T cell Activator STEMCELL Technologies Cat# 10971; RRID: AB_2827806 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXcell Cat# BE0012; RRID: AB_1107619 Bacterial and virus strains DH5α Thermo Fisher Scientific 18265017 Biological samples Healthy people peripheral blood mononuclear cells Tsinghua University N/A Ankylosing spondylitis people peripheral blood mononuclear cells West China Hospital N/A Systemic lupus erythematosus people peripheral blood mononuclear cells West China Hospital N/A Chemicals, peptides, and recombinant proteins RPMI 1640 medium Macgene CM10041 DMEM medium Macgene CM10013 HBSS, without calcium and magnesium Macgene CC016 10×HBSS, without calcium and magnesium Macgene CC016.1 Penicillin-Streptomycin Macgene CC004 Trypsin-EDTA (0.25%), phenol red Macgene CC017 Human TGF-β1 R&D 240-B; GenPept: P01137 Trizol Thermo Scientific 15596 Lipofectamine 2000 Transfection Reagent Thermo Scientific 11668027 FBS Gemini 900–108 Sodium Propionate Sigma-Aldrich P1880 Sodium Succinate Sigma-Aldrich S9637 Sodium Acetate Sigma-Aldrich S5636 anti-FLAG M2 affinity gel Sigma-Aldrich A2220 Polybrene Sigma-Aldrich AL-118 2-Mercaptoethanol Sigma-Aldrich M3148 Brefeldin A Solution Invitrogen 00-4506-51 Monensin Solution Invitrogen 00-4505-51 DAPI Invitrogen D3571 Recombinant Mouse IL-2 Novoprotein CK24 Recombinant Human IL-2 Novoprotein C013 Phosphate-Buffered Saline, without calcium and magnesium Corning 21-040-CV rProtein G MagBeads Yeasen 36419ES03 (Continued on next page) 18 Cell Reports 45, 117084, March 24, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dextran Sulfate Sodium Salt Yeasen 60316ES60 Hieff Trans® Polyethylenimine Linear (PEI) Yeasen 40816ES02 EDTA-free protease inhibitor cocktail Yeasen 20124ES10 FX1 MedChemExpress HY-102027 APG-115 MedChemExpress HY-101518 nutlin-3 MedChemExpress HY-50696 Pifithrin-α hydrobromide MedChemExpress HY-15484 A-485 MedChemExpress HY-107455 Critical commercial assays KOD OneTM PCR Master Mix TOYOBO KMM-101 ReverTra Ace qPCR RT Master Mix with gDNA Remover TOYOBO FSQ-301 Zombie YellowTM Fixable Viability Kit Biolegend 423104 Percoll GE Healthcare 17089101 Ficoll-Paque PLUS GE Healthcare 17144002 Fixation/Permeabilization Diluent Invitrogen 00-5223-56 Fixation/Permeabilization Concentrate Invitrogen 00-5123-43 2×HieffTM PCR Master Mix (With Dye) Yeasen 10102ES08 NovoStart® SYBR qPCR SuperMix Plus Novoprotein E096-01A Mouse IL-6 ELISA Kit CUSABIO CSB-E04639m Mouse IgE ELISA Kit CUSABIO CSB-E07983m Mouse TNF-α ELISA Kit CUSABIO CSB-E04741m Mouse MCP-1/MCAF ELISA Kit CUSABIO CSB-E07430m Dual-Luciferase® Reporter Assay System Promega E1910 EasySepTM Mouse CD4+ T cell Isolation Kit STEMCELL Technologies 19852 EasySepTM Mouse CD25 Regulatory T cell Positive Selection Kit STEMCELL Technologies 18782 EasySepTM Human CD4+CD127lowCD25+ Regulatory T cell Isolation Kit STEMCELL Technologies 18063 EasySepTM Mouse Biotin Positive Selection kit STEMCELL Technologies 17665 Deposited data Metabolomics data This paper MetaboLights: MTBLS13473 Mass spectrometry-based proteomic data This paper iProX: PXD071798 RNA sequencing data This paper GSA: CRA035222 CUT-Tag sequencing data This paper GSA: CRA037882 Raw Western Blots on Mendeley This paper Mendeley Data; https://doi.org/10.17632/ tk3cn3rhb8.4 Experimental models: Cell lines HEK293T ATCC Cat#CRL-3216; RRID: CVCL_0063 MEF This paper N/A Experimental models: Organisms/strains C57BL/6 mice Animal facility at Tsinghua University N/A Cd4Cre mice This study N/A Foxp3Cre mice This study N/A Aldh6a1flox/folx mice Shanghai Model Organism NM-CKO-234466 Trp53flox/flox mice This study N/A Rag1− /− mice This study N/A (Continued on next page) Cell Reports 45, 117084, March 24, 2026 19
Article Title: Regulatory T cell-derived TGF-β signaling governs the differentiation and maintenance of tumor-infiltrating bystander CD8 + T cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PerCP/Cyanine5.5 anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100734; RRID: AB_2075238 Brilliant Violet 510TM anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100752; RRID: AB_2563057 PE anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100707; RRID: AB_312746 PerCP/Cyanine5.5 anti-mouse CD44 (clone IM7) Biolegend Cat# 103032; RRID: AB_ 2076204 APC anti-mouse CD45.1 (clone A20) Biolegend Cat# 110713; RRID: AB_ 313502 Alexa Fluor® 700 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110724; RRID: AB_493733 PE/Cyanine7 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110729; RRID: AB_1134170 PE/Cyanine7 anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104418; RRID: AB_313103 Brilliant Violet 605TM anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104437; RRID: AB_11125577 Brilliant Violet 421TM anti-mouse CD127 (IL-7Rα) (clone A7R34) Biolegend Cat# 135027; RRID: AB_2563103 PE anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 164203; RRID: AB_2936560 FITC anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 104505; RRID: AB_313108 PerCP anti-mouse CD45.1 (clone A20) Biolegend Cat# 110725; RRID: AB_893347 Brilliant Violet 510TM anti-mouse CX3CR1 (clone SA011F11) Biolegend Cat# 149013; RRID: AB_2565697 APC anti-mouse Blimp-1 (clone 5E7) Biolegend Cat# 150007; RRID: AB_2728186 PE anti-mouse/human KLRG1 (MAFA) (clone 2F1) Biolegend Cat# 138407; RRID: AB_10574005 Alexa Fluor® 700 anti-mouse CD45.2 (clone 104) Biolegend Cat# 109822; RRID: AB_493731 Pacific BlueTM anti-mouse CD45.2 (clone 104) Biolegend Cat# 109819; RRID: AB_492873 Alexa Fluor® 700 anti-mouse FOXP3 (clone MF-14) Biolegend Cat# 126421; RRID: AB_2750492 FITC anti-mouse CD25 (clone 3C7) Biolegend Cat# 101907; RRID: AB_961210 PE anti-mouse CD103 (clone W19396D) Biolegend Cat# 110903; RRID: AB_2927994 PE/Cyanine7 anti-mouse CD186 (CXCR6) (clone SA051D1) Biolegend Cat# 151118; RRID: AB_2721669 PerCP/Cyanine5.5 anti-mouse CD49a (clone HMα) Biolegend Cat# 142611; RRID: AB_2750218 TCF1/TCF7 Rabbit mAb (clone C63D9) Cell Signaling Technology Cat# 2203; RRID: N/A (Continued on next page) Cell Reports 45, 117189, April 28, 2026 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER KLF2 Rabbit mAb (clone E2Z1H) Cell Signaling Technology Cat# 15306; RRID: N/A Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM 647 Thermofisher Cat# A-21245; RRID: AB_2535813 Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM Plus 488 Thermofisher Cat# A-32731TR; RRID: AB_2866491 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXCell Cat# BE0012; RRID: AB_1107619 T-Select H-2Db LCMV gp33 (C9M) Tetramer-KAVYNFATM-APC MBL Cat# TS-M512-2 T-Select H-2Db LCMV NP396 Tetramer-FQPQNGQFI-APC MBL Cat# TS-M513-2 H-2Db LCMV gp276-286 Tetramer-SGVENPGGYCL-APC MBL Cat# TS-5009-2 FITC anti-human CD45RA (clone HI100) Biolegend Cat# 304105; RRID: AB_314409 PerCP anti-human CD197 (CCR7) (clone G043H7) Biolegend Cat# 353241; RRID: AB_2564545 PE/Cyanine7 anti-human CD62L (clone S21001C) Biolegend Cat# 385109; RRID: AB_3683426 Alexa Fluor® 700 anti-human CD3 (clone OKT3) Biolegend Cat# 317339; RRID: AB_2563407 Brilliant Violet 605TM anti-human CD69 (clone FN50) Biolegend Cat# 310937; RRID: AB_2562306 Brilliant Violet 711TM anti-human CD8 (clone SK1) Biolegend Cat# 344733; RRID: AB_2565242 PE labeled Pro5 MHC Pentamers A*11:01 SIIPSGPLK PROIMMUNE Cat# 1513 Bacterial and virus strains LCMV Armstrong Dr. Rafi Ahmed N/A Listeria monocytogenes expressing ovalbumin (OVA) This lab N/A Biological samples Human CRC tumor specimens Xinqiao Hospital (Army Medical University) N/A Chemicals, peptides, and recombinant proteins Trypsin-EDTA (0.25%), phenol red Gibco Cat# 25200056 Fetal Bovine Serum (FBS) Gibco Cat# A5669701 RPMI 1640 Gibco Cat# 11875093 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 11965092 L-Glutamine 200mM (100×) Gibco Cat# 25030081 Non-Essential Amino Acids (MEM NEAA) (100×) Gibco Cat# 11140050 Sodium Pyruvate (100mM) Gibco Cat# 11360070 Dimethyl sulfoxide (DMSO) Sigma Cat# 20688 Diphtheria toxin Sigma Cat# D0564 Penicillin-Streptomycin-Glutamine Solution Gibco Cat# 10378016 β-Mercaptoethanol Procell Cat# PB180633 Percoll GE Healthcare Cat# 17-0891-09 FTY720 Merck Cat# SML0700 Peptide: KAVYNFATM (GP33-41) GL Biochem (Shanghai) Ltd Cat# 057477 Human Recombinant IL-2 Novoprotein Cat# C013 Polybrene Sigma-Aldrich Cat# TR-1003 (Continued on next page) 20 Cell Reports 45, 117189, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Gibco Cat# 31985070 TransIT-293 Mirus Cat# MIR 2706 Ficoll TBD Cat# LTS107701 collagenase I Diamond Cat# A004194 collagenase II Diamond Cat# A004174 LY2109761 MedChemExpress Cat# HY-12075 AgeI New England Biolabs Cat# R0552 EcoRI New England Biolabs Cat# R3101 T4 DNA Ligase New England Biolabs Cat# M0202 E. coli DH5α TransGen Cat# CD201 Critical commercial assays LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit Thermofisher Cat# L34975 Cytofix/Cytoperm Fixation/Permeabilization Kit BD Biosciences Cat# 554714; RRID: AB_2869008 FastPure Cell/Tissue Total RNA Isolation Kit V2 Vazyme Cat# RC112-01 RevertAid H Minus First Strand cDNA Synthesis Kit Thermofisher Cat# K1622 AceQ qPCR SYBR Green Master Mix Vazyme Cat# Q111 QIAprep Spin Miniprep Kit-Plasmid purification Qiagen Cat# 270106 MycAway® Mycoplasma Real-time qPCR Detection Kit Yeasen Cat# 40619ES25 Hyperactive ATAC-seq Library Prep Kit for Illumina Vazyme Cat# TD711 Deposited data Raw ATAC-seq data (TCM, TEM, and TRM subsets of TME-infiltrating P14 TBYS cells) This paper GEO: GSE306797 scRNA-seq data of P14 TBYS cells from MC38 TME Chen et al. 10 GEO: GSE222002 scRNA-seq data of P14 TMEM from lymphoid tissue Crowl et al. 24 GEO: GSE182276 scRNA-seq data of P14 TMEM from non-lymphoid tissue Kurd et al.25 GEO: GSE131847 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human CRC Chen et al.27 GEO: GSE236581 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human NSCLC Caushi et al.28 GEO: GSE173351 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human BCC Yost et al.40 GEO: GSE123813 ATAC-seq data of splenic naive P14 CD8+ T cells McDonald et al.32 GEO: GSE228381 ATAC-seq data of splenic P14 TCM and TEM cells Zhao et al. 33 GEO: GSE213041 ATAC-seq data of P14 TRM cell Crowl et al. 24 GEO: GSE182276 Experimental models: Cell lines B16F10 cells ATCC Cat# CRL-6475 MC38 cells Shanghai Model Organisms Center Cat# NM-S13 LLC cells ATCC Cat# CRL-1642 HEK293T cells ATCC Cat# CRL-3216 Experimental models: Organisms/strains Mouse: C57BL/6J (CD45.2) Jackson Laboratory Stock No: 000664 Mouse: C57BL/6-Tg (TcraTcrb) 1100Mjb/J (OT-1) Jackson Laboratory Stock No: 003831 Mouse: B6.Cg-Tcratm1Mom Tg (TcrLCMV) 327Sdz/TacMmjax (P14) From Dr. Rafi.
Transfection:Article Title: Loss of p53 exacerbates autoimmunity by reprogramming propionyl-CoA metabolism and histone modifications in Treg cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Anti-CD152-APC Biolegend Cat# 106310; RRID: AB_2087653 Mouse Anti-CD95 (Fas)-PE Biolegend Cat# 152608; RRID: AB_2632902 Mouse Anti-CD279 (PD-1)-PE Biolegend Cat# 135210; RRID: AB_2159183 Mouse Anti-CD185 (CXCR5)-PE Biolegend Cat# 145504; RRID: AB_2561967 Mouse/Human Anti-GL7Antigen-Pacific Blue Biolegend Cat# 144614; RRID: AB_2563291 Mouse anti-CD45.1-APC Biolegend Cat# 110714; RRID: AB_313503 Human Anti-CD4-Pacific Blue Biolegend Cat# 317424; RRID: AB_571953 Human Anti-CD8a-FITC Biolegend Cat# 301060; RRID: AB_2562055 Human Anti-IL-17A-PE Biolegend Cat# 512305; RRID: AB_961394 Human Anti-IFN-γ-APC Biolegend Cat# 512305; RRID: AB_961394 Human Anti-KLRG1-APC Biolegend Cat# 368605; RRID: AB_2571925 Human Anti-ICOS-FITC Biolegend Cat# 313506; RRID: AB_416329 Human CD3/CD28 T cell Activator STEMCELL Technologies Cat# 10971; RRID: AB_2827806 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXcell Cat# BE0012; RRID: AB_1107619 Bacterial and virus strains DH5α Thermo Fisher Scientific 18265017 Biological samples Healthy people peripheral blood mononuclear cells Tsinghua University N/A Ankylosing spondylitis people peripheral blood mononuclear cells West China Hospital N/A Systemic lupus erythematosus people peripheral blood mononuclear cells West China Hospital N/A Chemicals, peptides, and recombinant proteins RPMI 1640 medium Macgene CM10041 DMEM medium Macgene CM10013 HBSS, without calcium and magnesium Macgene CC016 10×HBSS, without calcium and magnesium Macgene CC016.1 Penicillin-Streptomycin Macgene CC004 Trypsin-EDTA (0.25%), phenol red Macgene CC017 Human TGF-β1 R&D 240-B; GenPept: P01137 Trizol Thermo Scientific 15596 Lipofectamine 2000 Transfection Reagent Thermo Scientific 11668027 FBS Gemini 900–108 Sodium Propionate Sigma-Aldrich P1880 Sodium Succinate Sigma-Aldrich S9637 Sodium Acetate Sigma-Aldrich S5636 anti-FLAG M2 affinity gel Sigma-Aldrich A2220 Polybrene Sigma-Aldrich AL-118 2-Mercaptoethanol Sigma-Aldrich M3148 Brefeldin A Solution Invitrogen 00-4506-51 Monensin Solution Invitrogen 00-4505-51 DAPI Invitrogen D3571 Recombinant Mouse IL-2 Novoprotein CK24 Recombinant Human IL-2 Novoprotein C013 Phosphate-Buffered Saline, without calcium and magnesium Corning 21-040-CV rProtein G MagBeads Yeasen 36419ES03 (Continued on next page) 18 Cell Reports 45, 117084, March 24, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dextran Sulfate Sodium Salt Yeasen 60316ES60 Hieff Trans® Polyethylenimine Linear (PEI) Yeasen 40816ES02 EDTA-free protease inhibitor cocktail Yeasen 20124ES10 FX1 MedChemExpress HY-102027 APG-115 MedChemExpress HY-101518 nutlin-3 MedChemExpress HY-50696 Pifithrin-α hydrobromide MedChemExpress HY-15484 A-485 MedChemExpress HY-107455 Critical commercial assays KOD OneTM PCR Master Mix TOYOBO KMM-101 ReverTra Ace qPCR RT Master Mix with gDNA Remover TOYOBO FSQ-301 Zombie YellowTM Fixable Viability Kit Biolegend 423104 Percoll GE Healthcare 17089101 Ficoll-Paque PLUS GE Healthcare 17144002 Fixation/Permeabilization Diluent Invitrogen 00-5223-56 Fixation/Permeabilization Concentrate Invitrogen 00-5123-43 2×HieffTM PCR Master Mix (With Dye) Yeasen 10102ES08 NovoStart® SYBR qPCR SuperMix Plus Novoprotein E096-01A Mouse IL-6 ELISA Kit CUSABIO CSB-E04639m Mouse IgE ELISA Kit CUSABIO CSB-E07983m Mouse TNF-α ELISA Kit CUSABIO CSB-E04741m Mouse MCP-1/MCAF ELISA Kit CUSABIO CSB-E07430m Dual-Luciferase® Reporter Assay System Promega E1910 EasySepTM Mouse CD4+ T cell Isolation Kit STEMCELL Technologies 19852 EasySepTM Mouse CD25 Regulatory T cell Positive Selection Kit STEMCELL Technologies 18782 EasySepTM Human CD4+CD127lowCD25+ Regulatory T cell Isolation Kit STEMCELL Technologies 18063 EasySepTM Mouse Biotin Positive Selection kit STEMCELL Technologies 17665 Deposited data Metabolomics data This paper MetaboLights: MTBLS13473 Mass spectrometry-based proteomic data This paper iProX: PXD071798 RNA sequencing data This paper GSA: CRA035222 CUT-Tag sequencing data This paper GSA: CRA037882 Raw Western Blots on Mendeley This paper Mendeley Data; https://doi.org/10.17632/ tk3cn3rhb8.4 Experimental models: Cell lines HEK293T ATCC Cat#CRL-3216; RRID: CVCL_0063 MEF This paper N/A Experimental models: Organisms/strains C57BL/6 mice Animal facility at Tsinghua University N/A Cd4Cre mice This study N/A Foxp3Cre mice This study N/A Aldh6a1flox/folx mice Shanghai Model Organism NM-CKO-234466 Trp53flox/flox mice This study N/A Rag1− /− mice This study N/A (Continued on next page) Cell Reports 45, 117084, March 24, 2026 19
Saline:Article Title: Loss of p53 exacerbates autoimmunity by reprogramming propionyl-CoA metabolism and histone modifications in Treg cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Anti-CD152-APC Biolegend Cat# 106310; RRID: AB_2087653 Mouse Anti-CD95 (Fas)-PE Biolegend Cat# 152608; RRID: AB_2632902 Mouse Anti-CD279 (PD-1)-PE Biolegend Cat# 135210; RRID: AB_2159183 Mouse Anti-CD185 (CXCR5)-PE Biolegend Cat# 145504; RRID: AB_2561967 Mouse/Human Anti-GL7Antigen-Pacific Blue Biolegend Cat# 144614; RRID: AB_2563291 Mouse anti-CD45.1-APC Biolegend Cat# 110714; RRID: AB_313503 Human Anti-CD4-Pacific Blue Biolegend Cat# 317424; RRID: AB_571953 Human Anti-CD8a-FITC Biolegend Cat# 301060; RRID: AB_2562055 Human Anti-IL-17A-PE Biolegend Cat# 512305; RRID: AB_961394 Human Anti-IFN-γ-APC Biolegend Cat# 512305; RRID: AB_961394 Human Anti-KLRG1-APC Biolegend Cat# 368605; RRID: AB_2571925 Human Anti-ICOS-FITC Biolegend Cat# 313506; RRID: AB_416329 Human CD3/CD28 T cell Activator STEMCELL Technologies Cat# 10971; RRID: AB_2827806 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXcell Cat# BE0012; RRID: AB_1107619 Bacterial and virus strains DH5α Thermo Fisher Scientific 18265017 Biological samples Healthy people peripheral blood mononuclear cells Tsinghua University N/A Ankylosing spondylitis people peripheral blood mononuclear cells West China Hospital N/A Systemic lupus erythematosus people peripheral blood mononuclear cells West China Hospital N/A Chemicals, peptides, and recombinant proteins RPMI 1640 medium Macgene CM10041 DMEM medium Macgene CM10013 HBSS, without calcium and magnesium Macgene CC016 10×HBSS, without calcium and magnesium Macgene CC016.1 Penicillin-Streptomycin Macgene CC004 Trypsin-EDTA (0.25%), phenol red Macgene CC017 Human TGF-β1 R&D 240-B; GenPept: P01137 Trizol Thermo Scientific 15596 Lipofectamine 2000 Transfection Reagent Thermo Scientific 11668027 FBS Gemini 900–108 Sodium Propionate Sigma-Aldrich P1880 Sodium Succinate Sigma-Aldrich S9637 Sodium Acetate Sigma-Aldrich S5636 anti-FLAG M2 affinity gel Sigma-Aldrich A2220 Polybrene Sigma-Aldrich AL-118 2-Mercaptoethanol Sigma-Aldrich M3148 Brefeldin A Solution Invitrogen 00-4506-51 Monensin Solution Invitrogen 00-4505-51 DAPI Invitrogen D3571 Recombinant Mouse IL-2 Novoprotein CK24 Recombinant Human IL-2 Novoprotein C013 Phosphate-Buffered Saline, without calcium and magnesium Corning 21-040-CV rProtein G MagBeads Yeasen 36419ES03 (Continued on next page) 18 Cell Reports 45, 117084, March 24, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dextran Sulfate Sodium Salt Yeasen 60316ES60 Hieff Trans® Polyethylenimine Linear (PEI) Yeasen 40816ES02 EDTA-free protease inhibitor cocktail Yeasen 20124ES10 FX1 MedChemExpress HY-102027 APG-115 MedChemExpress HY-101518 nutlin-3 MedChemExpress HY-50696 Pifithrin-α hydrobromide MedChemExpress HY-15484 A-485 MedChemExpress HY-107455 Critical commercial assays KOD OneTM PCR Master Mix TOYOBO KMM-101 ReverTra Ace qPCR RT Master Mix with gDNA Remover TOYOBO FSQ-301 Zombie YellowTM Fixable Viability Kit Biolegend 423104 Percoll GE Healthcare 17089101 Ficoll-Paque PLUS GE Healthcare 17144002 Fixation/Permeabilization Diluent Invitrogen 00-5223-56 Fixation/Permeabilization Concentrate Invitrogen 00-5123-43 2×HieffTM PCR Master Mix (With Dye) Yeasen 10102ES08 NovoStart® SYBR qPCR SuperMix Plus Novoprotein E096-01A Mouse IL-6 ELISA Kit CUSABIO CSB-E04639m Mouse IgE ELISA Kit CUSABIO CSB-E07983m Mouse TNF-α ELISA Kit CUSABIO CSB-E04741m Mouse MCP-1/MCAF ELISA Kit CUSABIO CSB-E07430m Dual-Luciferase® Reporter Assay System Promega E1910 EasySepTM Mouse CD4+ T cell Isolation Kit STEMCELL Technologies 19852 EasySepTM Mouse CD25 Regulatory T cell Positive Selection Kit STEMCELL Technologies 18782 EasySepTM Human CD4+CD127lowCD25+ Regulatory T cell Isolation Kit STEMCELL Technologies 18063 EasySepTM Mouse Biotin Positive Selection kit STEMCELL Technologies 17665 Deposited data Metabolomics data This paper MetaboLights: MTBLS13473 Mass spectrometry-based proteomic data This paper iProX: PXD071798 RNA sequencing data This paper GSA: CRA035222 CUT-Tag sequencing data This paper GSA: CRA037882 Raw Western Blots on Mendeley This paper Mendeley Data; https://doi.org/10.17632/ tk3cn3rhb8.4 Experimental models: Cell lines HEK293T ATCC Cat#CRL-3216; RRID: CVCL_0063 MEF This paper N/A Experimental models: Organisms/strains C57BL/6 mice Animal facility at Tsinghua University N/A Cd4Cre mice This study N/A Foxp3Cre mice This study N/A Aldh6a1flox/folx mice Shanghai Model Organism NM-CKO-234466 Trp53flox/flox mice This study N/A Rag1− /− mice This study N/A (Continued on next page) Cell Reports 45, 117084, March 24, 2026 19
Purification:Article Title: CCR4 and CCR7 differentially regulate thymocyte localization with distinct outcomes for central tolerance
Article Snippet: antibody , Purified Rat anti-mouse CD8, Rat monoclonal, clone 53.6.72 , BioXCell , Cat # BE0004-1 , (1:100). .. antibody , Purified Rat anti-mouse CD25, Rat monoclonal, clone PC-61.5.3 , BioXCell , Cat # BE0012 , (1:100). .. antibody , Purified Rat anti-mouse CD11b, Rat monoclonal, clone M1/70 , BioXCell , Cat # BE0007 , (1:100).
Labeling:Article Title: Regulatory T cell-derived TGF-β signaling governs the differentiation and maintenance of tumor-infiltrating bystander CD8 + T cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PerCP/Cyanine5.5 anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100734; RRID: AB_2075238 Brilliant Violet 510TM anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100752; RRID: AB_2563057 PE anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100707; RRID: AB_312746 PerCP/Cyanine5.5 anti-mouse CD44 (clone IM7) Biolegend Cat# 103032; RRID: AB_ 2076204 APC anti-mouse CD45.1 (clone A20) Biolegend Cat# 110713; RRID: AB_ 313502 Alexa Fluor® 700 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110724; RRID: AB_493733 PE/Cyanine7 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110729; RRID: AB_1134170 PE/Cyanine7 anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104418; RRID: AB_313103 Brilliant Violet 605TM anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104437; RRID: AB_11125577 Brilliant Violet 421TM anti-mouse CD127 (IL-7Rα) (clone A7R34) Biolegend Cat# 135027; RRID: AB_2563103 PE anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 164203; RRID: AB_2936560 FITC anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 104505; RRID: AB_313108 PerCP anti-mouse CD45.1 (clone A20) Biolegend Cat# 110725; RRID: AB_893347 Brilliant Violet 510TM anti-mouse CX3CR1 (clone SA011F11) Biolegend Cat# 149013; RRID: AB_2565697 APC anti-mouse Blimp-1 (clone 5E7) Biolegend Cat# 150007; RRID: AB_2728186 PE anti-mouse/human KLRG1 (MAFA) (clone 2F1) Biolegend Cat# 138407; RRID: AB_10574005 Alexa Fluor® 700 anti-mouse CD45.2 (clone 104) Biolegend Cat# 109822; RRID: AB_493731 Pacific BlueTM anti-mouse CD45.2 (clone 104) Biolegend Cat# 109819; RRID: AB_492873 Alexa Fluor® 700 anti-mouse FOXP3 (clone MF-14) Biolegend Cat# 126421; RRID: AB_2750492 FITC anti-mouse CD25 (clone 3C7) Biolegend Cat# 101907; RRID: AB_961210 PE anti-mouse CD103 (clone W19396D) Biolegend Cat# 110903; RRID: AB_2927994 PE/Cyanine7 anti-mouse CD186 (CXCR6) (clone SA051D1) Biolegend Cat# 151118; RRID: AB_2721669 PerCP/Cyanine5.5 anti-mouse CD49a (clone HMα) Biolegend Cat# 142611; RRID: AB_2750218 TCF1/TCF7 Rabbit mAb (clone C63D9) Cell Signaling Technology Cat# 2203; RRID: N/A (Continued on next page) Cell Reports 45, 117189, April 28, 2026 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER KLF2 Rabbit mAb (clone E2Z1H) Cell Signaling Technology Cat# 15306; RRID: N/A Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM 647 Thermofisher Cat# A-21245; RRID: AB_2535813 Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM Plus 488 Thermofisher Cat# A-32731TR; RRID: AB_2866491 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXCell Cat# BE0012; RRID: AB_1107619 T-Select H-2Db LCMV gp33 (C9M) Tetramer-KAVYNFATM-APC MBL Cat# TS-M512-2 T-Select H-2Db LCMV NP396 Tetramer-FQPQNGQFI-APC MBL Cat# TS-M513-2 H-2Db LCMV gp276-286 Tetramer-SGVENPGGYCL-APC MBL Cat# TS-5009-2 FITC anti-human CD45RA (clone HI100) Biolegend Cat# 304105; RRID: AB_314409 PerCP anti-human CD197 (CCR7) (clone G043H7) Biolegend Cat# 353241; RRID: AB_2564545 PE/Cyanine7 anti-human CD62L (clone S21001C) Biolegend Cat# 385109; RRID: AB_3683426 Alexa Fluor® 700 anti-human CD3 (clone OKT3) Biolegend Cat# 317339; RRID: AB_2563407 Brilliant Violet 605TM anti-human CD69 (clone FN50) Biolegend Cat# 310937; RRID: AB_2562306 Brilliant Violet 711TM anti-human CD8 (clone SK1) Biolegend Cat# 344733; RRID: AB_2565242 PE labeled Pro5 MHC Pentamers A*11:01 SIIPSGPLK PROIMMUNE Cat# 1513 Bacterial and virus strains LCMV Armstrong Dr. Rafi Ahmed N/A Listeria monocytogenes expressing ovalbumin (OVA) This lab N/A Biological samples Human CRC tumor specimens Xinqiao Hospital (Army Medical University) N/A Chemicals, peptides, and recombinant proteins Trypsin-EDTA (0.25%), phenol red Gibco Cat# 25200056 Fetal Bovine Serum (FBS) Gibco Cat# A5669701 RPMI 1640 Gibco Cat# 11875093 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 11965092 L-Glutamine 200mM (100×) Gibco Cat# 25030081 Non-Essential Amino Acids (MEM NEAA) (100×) Gibco Cat# 11140050 Sodium Pyruvate (100mM) Gibco Cat# 11360070 Dimethyl sulfoxide (DMSO) Sigma Cat# 20688 Diphtheria toxin Sigma Cat# D0564 Penicillin-Streptomycin-Glutamine Solution Gibco Cat# 10378016 β-Mercaptoethanol Procell Cat# PB180633 Percoll GE Healthcare Cat# 17-0891-09 FTY720 Merck Cat# SML0700 Peptide: KAVYNFATM (GP33-41) GL Biochem (Shanghai) Ltd Cat# 057477 Human Recombinant IL-2 Novoprotein Cat# C013 Polybrene Sigma-Aldrich Cat# TR-1003 (Continued on next page) 20 Cell Reports 45, 117189, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Gibco Cat# 31985070 TransIT-293 Mirus Cat# MIR 2706 Ficoll TBD Cat# LTS107701 collagenase I Diamond Cat# A004194 collagenase II Diamond Cat# A004174 LY2109761 MedChemExpress Cat# HY-12075 AgeI New England Biolabs Cat# R0552 EcoRI New England Biolabs Cat# R3101 T4 DNA Ligase New England Biolabs Cat# M0202 E. coli DH5α TransGen Cat# CD201 Critical commercial assays LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit Thermofisher Cat# L34975 Cytofix/Cytoperm Fixation/Permeabilization Kit BD Biosciences Cat# 554714; RRID: AB_2869008 FastPure Cell/Tissue Total RNA Isolation Kit V2 Vazyme Cat# RC112-01 RevertAid H Minus First Strand cDNA Synthesis Kit Thermofisher Cat# K1622 AceQ qPCR SYBR Green Master Mix Vazyme Cat# Q111 QIAprep Spin Miniprep Kit-Plasmid purification Qiagen Cat# 270106 MycAway® Mycoplasma Real-time qPCR Detection Kit Yeasen Cat# 40619ES25 Hyperactive ATAC-seq Library Prep Kit for Illumina Vazyme Cat# TD711 Deposited data Raw ATAC-seq data (TCM, TEM, and TRM subsets of TME-infiltrating P14 TBYS cells) This paper GEO: GSE306797 scRNA-seq data of P14 TBYS cells from MC38 TME Chen et al. 10 GEO: GSE222002 scRNA-seq data of P14 TMEM from lymphoid tissue Crowl et al. 24 GEO: GSE182276 scRNA-seq data of P14 TMEM from non-lymphoid tissue Kurd et al.25 GEO: GSE131847 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human CRC Chen et al.27 GEO: GSE236581 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human NSCLC Caushi et al.28 GEO: GSE173351 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human BCC Yost et al.40 GEO: GSE123813 ATAC-seq data of splenic naive P14 CD8+ T cells McDonald et al.32 GEO: GSE228381 ATAC-seq data of splenic P14 TCM and TEM cells Zhao et al. 33 GEO: GSE213041 ATAC-seq data of P14 TRM cell Crowl et al. 24 GEO: GSE182276 Experimental models: Cell lines B16F10 cells ATCC Cat# CRL-6475 MC38 cells Shanghai Model Organisms Center Cat# NM-S13 LLC cells ATCC Cat# CRL-1642 HEK293T cells ATCC Cat# CRL-3216 Experimental models: Organisms/strains Mouse: C57BL/6J (CD45.2) Jackson Laboratory Stock No: 000664 Mouse: C57BL/6-Tg (TcraTcrb) 1100Mjb/J (OT-1) Jackson Laboratory Stock No: 003831 Mouse: B6.Cg-Tcratm1Mom Tg (TcrLCMV) 327Sdz/TacMmjax (P14) From Dr. Rafi.
Immunopeptidomics:Article Title: Regulatory T cell-derived TGF-β signaling governs the differentiation and maintenance of tumor-infiltrating bystander CD8 + T cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PerCP/Cyanine5.5 anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100734; RRID: AB_2075238 Brilliant Violet 510TM anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100752; RRID: AB_2563057 PE anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100707; RRID: AB_312746 PerCP/Cyanine5.5 anti-mouse CD44 (clone IM7) Biolegend Cat# 103032; RRID: AB_ 2076204 APC anti-mouse CD45.1 (clone A20) Biolegend Cat# 110713; RRID: AB_ 313502 Alexa Fluor® 700 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110724; RRID: AB_493733 PE/Cyanine7 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110729; RRID: AB_1134170 PE/Cyanine7 anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104418; RRID: AB_313103 Brilliant Violet 605TM anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104437; RRID: AB_11125577 Brilliant Violet 421TM anti-mouse CD127 (IL-7Rα) (clone A7R34) Biolegend Cat# 135027; RRID: AB_2563103 PE anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 164203; RRID: AB_2936560 FITC anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 104505; RRID: AB_313108 PerCP anti-mouse CD45.1 (clone A20) Biolegend Cat# 110725; RRID: AB_893347 Brilliant Violet 510TM anti-mouse CX3CR1 (clone SA011F11) Biolegend Cat# 149013; RRID: AB_2565697 APC anti-mouse Blimp-1 (clone 5E7) Biolegend Cat# 150007; RRID: AB_2728186 PE anti-mouse/human KLRG1 (MAFA) (clone 2F1) Biolegend Cat# 138407; RRID: AB_10574005 Alexa Fluor® 700 anti-mouse CD45.2 (clone 104) Biolegend Cat# 109822; RRID: AB_493731 Pacific BlueTM anti-mouse CD45.2 (clone 104) Biolegend Cat# 109819; RRID: AB_492873 Alexa Fluor® 700 anti-mouse FOXP3 (clone MF-14) Biolegend Cat# 126421; RRID: AB_2750492 FITC anti-mouse CD25 (clone 3C7) Biolegend Cat# 101907; RRID: AB_961210 PE anti-mouse CD103 (clone W19396D) Biolegend Cat# 110903; RRID: AB_2927994 PE/Cyanine7 anti-mouse CD186 (CXCR6) (clone SA051D1) Biolegend Cat# 151118; RRID: AB_2721669 PerCP/Cyanine5.5 anti-mouse CD49a (clone HMα) Biolegend Cat# 142611; RRID: AB_2750218 TCF1/TCF7 Rabbit mAb (clone C63D9) Cell Signaling Technology Cat# 2203; RRID: N/A (Continued on next page) Cell Reports 45, 117189, April 28, 2026 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER KLF2 Rabbit mAb (clone E2Z1H) Cell Signaling Technology Cat# 15306; RRID: N/A Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM 647 Thermofisher Cat# A-21245; RRID: AB_2535813 Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM Plus 488 Thermofisher Cat# A-32731TR; RRID: AB_2866491 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXCell Cat# BE0012; RRID: AB_1107619 T-Select H-2Db LCMV gp33 (C9M) Tetramer-KAVYNFATM-APC MBL Cat# TS-M512-2 T-Select H-2Db LCMV NP396 Tetramer-FQPQNGQFI-APC MBL Cat# TS-M513-2 H-2Db LCMV gp276-286 Tetramer-SGVENPGGYCL-APC MBL Cat# TS-5009-2 FITC anti-human CD45RA (clone HI100) Biolegend Cat# 304105; RRID: AB_314409 PerCP anti-human CD197 (CCR7) (clone G043H7) Biolegend Cat# 353241; RRID: AB_2564545 PE/Cyanine7 anti-human CD62L (clone S21001C) Biolegend Cat# 385109; RRID: AB_3683426 Alexa Fluor® 700 anti-human CD3 (clone OKT3) Biolegend Cat# 317339; RRID: AB_2563407 Brilliant Violet 605TM anti-human CD69 (clone FN50) Biolegend Cat# 310937; RRID: AB_2562306 Brilliant Violet 711TM anti-human CD8 (clone SK1) Biolegend Cat# 344733; RRID: AB_2565242 PE labeled Pro5 MHC Pentamers A*11:01 SIIPSGPLK PROIMMUNE Cat# 1513 Bacterial and virus strains LCMV Armstrong Dr. Rafi Ahmed N/A Listeria monocytogenes expressing ovalbumin (OVA) This lab N/A Biological samples Human CRC tumor specimens Xinqiao Hospital (Army Medical University) N/A Chemicals, peptides, and recombinant proteins Trypsin-EDTA (0.25%), phenol red Gibco Cat# 25200056 Fetal Bovine Serum (FBS) Gibco Cat# A5669701 RPMI 1640 Gibco Cat# 11875093 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 11965092 L-Glutamine 200mM (100×) Gibco Cat# 25030081 Non-Essential Amino Acids (MEM NEAA) (100×) Gibco Cat# 11140050 Sodium Pyruvate (100mM) Gibco Cat# 11360070 Dimethyl sulfoxide (DMSO) Sigma Cat# 20688 Diphtheria toxin Sigma Cat# D0564 Penicillin-Streptomycin-Glutamine Solution Gibco Cat# 10378016 β-Mercaptoethanol Procell Cat# PB180633 Percoll GE Healthcare Cat# 17-0891-09 FTY720 Merck Cat# SML0700 Peptide: KAVYNFATM (GP33-41) GL Biochem (Shanghai) Ltd Cat# 057477 Human Recombinant IL-2 Novoprotein Cat# C013 Polybrene Sigma-Aldrich Cat# TR-1003 (Continued on next page) 20 Cell Reports 45, 117189, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Gibco Cat# 31985070 TransIT-293 Mirus Cat# MIR 2706 Ficoll TBD Cat# LTS107701 collagenase I Diamond Cat# A004194 collagenase II Diamond Cat# A004174 LY2109761 MedChemExpress Cat# HY-12075 AgeI New England Biolabs Cat# R0552 EcoRI New England Biolabs Cat# R3101 T4 DNA Ligase New England Biolabs Cat# M0202 E. coli DH5α TransGen Cat# CD201 Critical commercial assays LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit Thermofisher Cat# L34975 Cytofix/Cytoperm Fixation/Permeabilization Kit BD Biosciences Cat# 554714; RRID: AB_2869008 FastPure Cell/Tissue Total RNA Isolation Kit V2 Vazyme Cat# RC112-01 RevertAid H Minus First Strand cDNA Synthesis Kit Thermofisher Cat# K1622 AceQ qPCR SYBR Green Master Mix Vazyme Cat# Q111 QIAprep Spin Miniprep Kit-Plasmid purification Qiagen Cat# 270106 MycAway® Mycoplasma Real-time qPCR Detection Kit Yeasen Cat# 40619ES25 Hyperactive ATAC-seq Library Prep Kit for Illumina Vazyme Cat# TD711 Deposited data Raw ATAC-seq data (TCM, TEM, and TRM subsets of TME-infiltrating P14 TBYS cells) This paper GEO: GSE306797 scRNA-seq data of P14 TBYS cells from MC38 TME Chen et al. 10 GEO: GSE222002 scRNA-seq data of P14 TMEM from lymphoid tissue Crowl et al. 24 GEO: GSE182276 scRNA-seq data of P14 TMEM from non-lymphoid tissue Kurd et al.25 GEO: GSE131847 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human CRC Chen et al.27 GEO: GSE236581 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human NSCLC Caushi et al.28 GEO: GSE173351 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human BCC Yost et al.40 GEO: GSE123813 ATAC-seq data of splenic naive P14 CD8+ T cells McDonald et al.32 GEO: GSE228381 ATAC-seq data of splenic P14 TCM and TEM cells Zhao et al. 33 GEO: GSE213041 ATAC-seq data of P14 TRM cell Crowl et al. 24 GEO: GSE182276 Experimental models: Cell lines B16F10 cells ATCC Cat# CRL-6475 MC38 cells Shanghai Model Organisms Center Cat# NM-S13 LLC cells ATCC Cat# CRL-1642 HEK293T cells ATCC Cat# CRL-3216 Experimental models: Organisms/strains Mouse: C57BL/6J (CD45.2) Jackson Laboratory Stock No: 000664 Mouse: C57BL/6-Tg (TcraTcrb) 1100Mjb/J (OT-1) Jackson Laboratory Stock No: 003831 Mouse: B6.Cg-Tcratm1Mom Tg (TcrLCMV) 327Sdz/TacMmjax (P14) From Dr. Rafi.
Expressing:Article Title: Regulatory T cell-derived TGF-β signaling governs the differentiation and maintenance of tumor-infiltrating bystander CD8 + T cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PerCP/Cyanine5.5 anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100734; RRID: AB_2075238 Brilliant Violet 510TM anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100752; RRID: AB_2563057 PE anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100707; RRID: AB_312746 PerCP/Cyanine5.5 anti-mouse CD44 (clone IM7) Biolegend Cat# 103032; RRID: AB_ 2076204 APC anti-mouse CD45.1 (clone A20) Biolegend Cat# 110713; RRID: AB_ 313502 Alexa Fluor® 700 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110724; RRID: AB_493733 PE/Cyanine7 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110729; RRID: AB_1134170 PE/Cyanine7 anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104418; RRID: AB_313103 Brilliant Violet 605TM anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104437; RRID: AB_11125577 Brilliant Violet 421TM anti-mouse CD127 (IL-7Rα) (clone A7R34) Biolegend Cat# 135027; RRID: AB_2563103 PE anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 164203; RRID: AB_2936560 FITC anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 104505; RRID: AB_313108 PerCP anti-mouse CD45.1 (clone A20) Biolegend Cat# 110725; RRID: AB_893347 Brilliant Violet 510TM anti-mouse CX3CR1 (clone SA011F11) Biolegend Cat# 149013; RRID: AB_2565697 APC anti-mouse Blimp-1 (clone 5E7) Biolegend Cat# 150007; RRID: AB_2728186 PE anti-mouse/human KLRG1 (MAFA) (clone 2F1) Biolegend Cat# 138407; RRID: AB_10574005 Alexa Fluor® 700 anti-mouse CD45.2 (clone 104) Biolegend Cat# 109822; RRID: AB_493731 Pacific BlueTM anti-mouse CD45.2 (clone 104) Biolegend Cat# 109819; RRID: AB_492873 Alexa Fluor® 700 anti-mouse FOXP3 (clone MF-14) Biolegend Cat# 126421; RRID: AB_2750492 FITC anti-mouse CD25 (clone 3C7) Biolegend Cat# 101907; RRID: AB_961210 PE anti-mouse CD103 (clone W19396D) Biolegend Cat# 110903; RRID: AB_2927994 PE/Cyanine7 anti-mouse CD186 (CXCR6) (clone SA051D1) Biolegend Cat# 151118; RRID: AB_2721669 PerCP/Cyanine5.5 anti-mouse CD49a (clone HMα) Biolegend Cat# 142611; RRID: AB_2750218 TCF1/TCF7 Rabbit mAb (clone C63D9) Cell Signaling Technology Cat# 2203; RRID: N/A (Continued on next page) Cell Reports 45, 117189, April 28, 2026 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER KLF2 Rabbit mAb (clone E2Z1H) Cell Signaling Technology Cat# 15306; RRID: N/A Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM 647 Thermofisher Cat# A-21245; RRID: AB_2535813 Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM Plus 488 Thermofisher Cat# A-32731TR; RRID: AB_2866491 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXCell Cat# BE0012; RRID: AB_1107619 T-Select H-2Db LCMV gp33 (C9M) Tetramer-KAVYNFATM-APC MBL Cat# TS-M512-2 T-Select H-2Db LCMV NP396 Tetramer-FQPQNGQFI-APC MBL Cat# TS-M513-2 H-2Db LCMV gp276-286 Tetramer-SGVENPGGYCL-APC MBL Cat# TS-5009-2 FITC anti-human CD45RA (clone HI100) Biolegend Cat# 304105; RRID: AB_314409 PerCP anti-human CD197 (CCR7) (clone G043H7) Biolegend Cat# 353241; RRID: AB_2564545 PE/Cyanine7 anti-human CD62L (clone S21001C) Biolegend Cat# 385109; RRID: AB_3683426 Alexa Fluor® 700 anti-human CD3 (clone OKT3) Biolegend Cat# 317339; RRID: AB_2563407 Brilliant Violet 605TM anti-human CD69 (clone FN50) Biolegend Cat# 310937; RRID: AB_2562306 Brilliant Violet 711TM anti-human CD8 (clone SK1) Biolegend Cat# 344733; RRID: AB_2565242 PE labeled Pro5 MHC Pentamers A*11:01 SIIPSGPLK PROIMMUNE Cat# 1513 Bacterial and virus strains LCMV Armstrong Dr. Rafi Ahmed N/A Listeria monocytogenes expressing ovalbumin (OVA) This lab N/A Biological samples Human CRC tumor specimens Xinqiao Hospital (Army Medical University) N/A Chemicals, peptides, and recombinant proteins Trypsin-EDTA (0.25%), phenol red Gibco Cat# 25200056 Fetal Bovine Serum (FBS) Gibco Cat# A5669701 RPMI 1640 Gibco Cat# 11875093 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 11965092 L-Glutamine 200mM (100×) Gibco Cat# 25030081 Non-Essential Amino Acids (MEM NEAA) (100×) Gibco Cat# 11140050 Sodium Pyruvate (100mM) Gibco Cat# 11360070 Dimethyl sulfoxide (DMSO) Sigma Cat# 20688 Diphtheria toxin Sigma Cat# D0564 Penicillin-Streptomycin-Glutamine Solution Gibco Cat# 10378016 β-Mercaptoethanol Procell Cat# PB180633 Percoll GE Healthcare Cat# 17-0891-09 FTY720 Merck Cat# SML0700 Peptide: KAVYNFATM (GP33-41) GL Biochem (Shanghai) Ltd Cat# 057477 Human Recombinant IL-2 Novoprotein Cat# C013 Polybrene Sigma-Aldrich Cat# TR-1003 (Continued on next page) 20 Cell Reports 45, 117189, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Gibco Cat# 31985070 TransIT-293 Mirus Cat# MIR 2706 Ficoll TBD Cat# LTS107701 collagenase I Diamond Cat# A004194 collagenase II Diamond Cat# A004174 LY2109761 MedChemExpress Cat# HY-12075 AgeI New England Biolabs Cat# R0552 EcoRI New England Biolabs Cat# R3101 T4 DNA Ligase New England Biolabs Cat# M0202 E. coli DH5α TransGen Cat# CD201 Critical commercial assays LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit Thermofisher Cat# L34975 Cytofix/Cytoperm Fixation/Permeabilization Kit BD Biosciences Cat# 554714; RRID: AB_2869008 FastPure Cell/Tissue Total RNA Isolation Kit V2 Vazyme Cat# RC112-01 RevertAid H Minus First Strand cDNA Synthesis Kit Thermofisher Cat# K1622 AceQ qPCR SYBR Green Master Mix Vazyme Cat# Q111 QIAprep Spin Miniprep Kit-Plasmid purification Qiagen Cat# 270106 MycAway® Mycoplasma Real-time qPCR Detection Kit Yeasen Cat# 40619ES25 Hyperactive ATAC-seq Library Prep Kit for Illumina Vazyme Cat# TD711 Deposited data Raw ATAC-seq data (TCM, TEM, and TRM subsets of TME-infiltrating P14 TBYS cells) This paper GEO: GSE306797 scRNA-seq data of P14 TBYS cells from MC38 TME Chen et al. 10 GEO: GSE222002 scRNA-seq data of P14 TMEM from lymphoid tissue Crowl et al. 24 GEO: GSE182276 scRNA-seq data of P14 TMEM from non-lymphoid tissue Kurd et al.25 GEO: GSE131847 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human CRC Chen et al.27 GEO: GSE236581 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human NSCLC Caushi et al.28 GEO: GSE173351 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human BCC Yost et al.40 GEO: GSE123813 ATAC-seq data of splenic naive P14 CD8+ T cells McDonald et al.32 GEO: GSE228381 ATAC-seq data of splenic P14 TCM and TEM cells Zhao et al. 33 GEO: GSE213041 ATAC-seq data of P14 TRM cell Crowl et al. 24 GEO: GSE182276 Experimental models: Cell lines B16F10 cells ATCC Cat# CRL-6475 MC38 cells Shanghai Model Organisms Center Cat# NM-S13 LLC cells ATCC Cat# CRL-1642 HEK293T cells ATCC Cat# CRL-3216 Experimental models: Organisms/strains Mouse: C57BL/6J (CD45.2) Jackson Laboratory Stock No: 000664 Mouse: C57BL/6-Tg (TcraTcrb) 1100Mjb/J (OT-1) Jackson Laboratory Stock No: 003831 Mouse: B6.Cg-Tcratm1Mom Tg (TcrLCMV) 327Sdz/TacMmjax (P14) From Dr. Rafi.
Modification:Article Title: Regulatory T cell-derived TGF-β signaling governs the differentiation and maintenance of tumor-infiltrating bystander CD8 + T cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies PerCP/Cyanine5.5 anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100734; RRID: AB_2075238 Brilliant Violet 510TM anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100752; RRID: AB_2563057 PE anti-mouse CD8a (clone 53–6.7) Biolegend Cat# 100707; RRID: AB_312746 PerCP/Cyanine5.5 anti-mouse CD44 (clone IM7) Biolegend Cat# 103032; RRID: AB_ 2076204 APC anti-mouse CD45.1 (clone A20) Biolegend Cat# 110713; RRID: AB_ 313502 Alexa Fluor® 700 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110724; RRID: AB_493733 PE/Cyanine7 anti-mouse CD45.1 (clone A20) Biolegend Cat# 110729; RRID: AB_1134170 PE/Cyanine7 anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104418; RRID: AB_313103 Brilliant Violet 605TM anti-mouse CD62L (clone MEL-14) Biolegend Cat# 104437; RRID: AB_11125577 Brilliant Violet 421TM anti-mouse CD127 (IL-7Rα) (clone A7R34) Biolegend Cat# 135027; RRID: AB_2563103 PE anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 164203; RRID: AB_2936560 FITC anti-mouse CD69 (clone H1.2F3) Biolegend Cat# 104505; RRID: AB_313108 PerCP anti-mouse CD45.1 (clone A20) Biolegend Cat# 110725; RRID: AB_893347 Brilliant Violet 510TM anti-mouse CX3CR1 (clone SA011F11) Biolegend Cat# 149013; RRID: AB_2565697 APC anti-mouse Blimp-1 (clone 5E7) Biolegend Cat# 150007; RRID: AB_2728186 PE anti-mouse/human KLRG1 (MAFA) (clone 2F1) Biolegend Cat# 138407; RRID: AB_10574005 Alexa Fluor® 700 anti-mouse CD45.2 (clone 104) Biolegend Cat# 109822; RRID: AB_493731 Pacific BlueTM anti-mouse CD45.2 (clone 104) Biolegend Cat# 109819; RRID: AB_492873 Alexa Fluor® 700 anti-mouse FOXP3 (clone MF-14) Biolegend Cat# 126421; RRID: AB_2750492 FITC anti-mouse CD25 (clone 3C7) Biolegend Cat# 101907; RRID: AB_961210 PE anti-mouse CD103 (clone W19396D) Biolegend Cat# 110903; RRID: AB_2927994 PE/Cyanine7 anti-mouse CD186 (CXCR6) (clone SA051D1) Biolegend Cat# 151118; RRID: AB_2721669 PerCP/Cyanine5.5 anti-mouse CD49a (clone HMα) Biolegend Cat# 142611; RRID: AB_2750218 TCF1/TCF7 Rabbit mAb (clone C63D9) Cell Signaling Technology Cat# 2203; RRID: N/A (Continued on next page) Cell Reports 45, 117189, April 28, 2026 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER KLF2 Rabbit mAb (clone E2Z1H) Cell Signaling Technology Cat# 15306; RRID: N/A Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM 647 Thermofisher Cat# A-21245; RRID: AB_2535813 Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody Alexa FluorTM Plus 488 Thermofisher Cat# A-32731TR; RRID: AB_2866491 InVivoMAb anti-mouse CD25 (IL-2Rα) BioXCell Cat# BE0012; RRID: AB_1107619 T-Select H-2Db LCMV gp33 (C9M) Tetramer-KAVYNFATM-APC MBL Cat# TS-M512-2 T-Select H-2Db LCMV NP396 Tetramer-FQPQNGQFI-APC MBL Cat# TS-M513-2 H-2Db LCMV gp276-286 Tetramer-SGVENPGGYCL-APC MBL Cat# TS-5009-2 FITC anti-human CD45RA (clone HI100) Biolegend Cat# 304105; RRID: AB_314409 PerCP anti-human CD197 (CCR7) (clone G043H7) Biolegend Cat# 353241; RRID: AB_2564545 PE/Cyanine7 anti-human CD62L (clone S21001C) Biolegend Cat# 385109; RRID: AB_3683426 Alexa Fluor® 700 anti-human CD3 (clone OKT3) Biolegend Cat# 317339; RRID: AB_2563407 Brilliant Violet 605TM anti-human CD69 (clone FN50) Biolegend Cat# 310937; RRID: AB_2562306 Brilliant Violet 711TM anti-human CD8 (clone SK1) Biolegend Cat# 344733; RRID: AB_2565242 PE labeled Pro5 MHC Pentamers A*11:01 SIIPSGPLK PROIMMUNE Cat# 1513 Bacterial and virus strains LCMV Armstrong Dr. Rafi Ahmed N/A Listeria monocytogenes expressing ovalbumin (OVA) This lab N/A Biological samples Human CRC tumor specimens Xinqiao Hospital (Army Medical University) N/A Chemicals, peptides, and recombinant proteins Trypsin-EDTA (0.25%), phenol red Gibco Cat# 25200056 Fetal Bovine Serum (FBS) Gibco Cat# A5669701 RPMI 1640 Gibco Cat# 11875093 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat# 11965092 L-Glutamine 200mM (100×) Gibco Cat# 25030081 Non-Essential Amino Acids (MEM NEAA) (100×) Gibco Cat# 11140050 Sodium Pyruvate (100mM) Gibco Cat# 11360070 Dimethyl sulfoxide (DMSO) Sigma Cat# 20688 Diphtheria toxin Sigma Cat# D0564 Penicillin-Streptomycin-Glutamine Solution Gibco Cat# 10378016 β-Mercaptoethanol Procell Cat# PB180633 Percoll GE Healthcare Cat# 17-0891-09 FTY720 Merck Cat# SML0700 Peptide: KAVYNFATM (GP33-41) GL Biochem (Shanghai) Ltd Cat# 057477 Human Recombinant IL-2 Novoprotein Cat# C013 Polybrene Sigma-Aldrich Cat# TR-1003 (Continued on next page) 20 Cell Reports 45, 117189, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Gibco Cat# 31985070 TransIT-293 Mirus Cat# MIR 2706 Ficoll TBD Cat# LTS107701 collagenase I Diamond Cat# A004194 collagenase II Diamond Cat# A004174 LY2109761 MedChemExpress Cat# HY-12075 AgeI New England Biolabs Cat# R0552 EcoRI New England Biolabs Cat# R3101 T4 DNA Ligase New England Biolabs Cat# M0202 E. coli DH5α TransGen Cat# CD201 Critical commercial assays LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit Thermofisher Cat# L34975 Cytofix/Cytoperm Fixation/Permeabilization Kit BD Biosciences Cat# 554714; RRID: AB_2869008 FastPure Cell/Tissue Total RNA Isolation Kit V2 Vazyme Cat# RC112-01 RevertAid H Minus First Strand cDNA Synthesis Kit Thermofisher Cat# K1622 AceQ qPCR SYBR Green Master Mix Vazyme Cat# Q111 QIAprep Spin Miniprep Kit-Plasmid purification Qiagen Cat# 270106 MycAway® Mycoplasma Real-time qPCR Detection Kit Yeasen Cat# 40619ES25 Hyperactive ATAC-seq Library Prep Kit for Illumina Vazyme Cat# TD711 Deposited data Raw ATAC-seq data (TCM, TEM, and TRM subsets of TME-infiltrating P14 TBYS cells) This paper GEO: GSE306797 scRNA-seq data of P14 TBYS cells from MC38 TME Chen et al. 10 GEO: GSE222002 scRNA-seq data of P14 TMEM from lymphoid tissue Crowl et al. 24 GEO: GSE182276 scRNA-seq data of P14 TMEM from non-lymphoid tissue Kurd et al.25 GEO: GSE131847 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human CRC Chen et al.27 GEO: GSE236581 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human NSCLC Caushi et al.28 GEO: GSE173351 scRNA-seq/scTCR-seq datasets of TME-infiltrating CD8+ T cells from human BCC Yost et al.40 GEO: GSE123813 ATAC-seq data of splenic naive P14 CD8+ T cells McDonald et al.32 GEO: GSE228381 ATAC-seq data of splenic P14 TCM and TEM cells Zhao et al. 33 GEO: GSE213041 ATAC-seq data of P14 TRM cell Crowl et al. 24 GEO: GSE182276 Experimental models: Cell lines B16F10 cells ATCC Cat# CRL-6475 MC38 cells Shanghai Model Organisms Center Cat# NM-S13 LLC cells ATCC Cat# CRL-1642 HEK293T cells ATCC Cat# CRL-3216 Experimental models: Organisms/strains Mouse: C57BL/6J (CD45.2) Jackson Laboratory Stock No: 000664 Mouse: C57BL/6-Tg (TcraTcrb) 1100Mjb/J (OT-1) Jackson Laboratory Stock No: 003831 Mouse: B6.Cg-Tcratm1Mom Tg (TcrLCMV) 327Sdz/TacMmjax (P14) From Dr. Rafi.
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