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|
|
| Antibodies |
| Ultra-LEAF™ Purified anti-mouse CD3ε Antibody (clone: 145–2C11) |
Biolegend |
Cat#100340 |
| Ultra-LEAF(TM) Purified anti-mouse CD28 Antibody (clone: 37.51) |
Biolegend |
Cat#102116 |
| APC anti-human CD3 Antibody (Clone: UCHT1) |
Biolegend |
Cat#300412 |
| FITC anti-human IgG Fc |
Biolegend |
Cat#409310 |
| PE anti-human IgG Fc (HP6017) |
Biolegend |
Cat#409304 |
| PE anti-DYKDDDDK Tag Antibody (L5) |
Biolegend |
Cat#637310 |
| APC/Cy7 anti-human CD8a antibody (HIT8a) |
Biolegend |
Cat#300926 |
| APC anti-human CD3 Antibody (Clone: HIT3a) |
Biolegend |
Cat#300312 |
| APC anti-mouse CD8a Antibody (53–6.7) |
Biolegend |
Cat#100712 |
| PE/Cy7 anti-mouse CD3ε Antibody (145–2C11) |
Biolegend |
Cat#100320 |
| PE anti-rat CD90/mouse CD90.1 (Thy-1.1) Antibody (OX-7) |
Biolegend |
Cat#202524 |
| PE anti-mouse CD107a (LAMP-1) Antibody (1D4B) |
Biolegend |
Cat#121612 |
| PE conjungate Cleaved Caspase-3 (Asp175) Rabbit mAb (5A1E) |
CST |
Cat#9978S |
| Brilliant Violet 510™ anti-human CD8 Antibody (SK1) |
Biolegend |
Cat#344732 |
| APC/Cy7 anti-human IFN-γ Antibody (4S.B3) |
Biolegend |
Cat#502530 |
| PE anti-human TNF-α Antibody (MAb11) |
Biolegend |
Cat#502909 |
| PerCP/Cyanine5.5 anti-human/mouse Granzyme B Recombinant Antibody (QA16A02) |
Biolegend |
Cat#372212 |
| APC anti-humanCD45RA Antibody (HI100) |
Biolegend |
Cat#304112 |
| PE/Cy7 anti-human CD62L Antibody (DREG-56) |
Biolegend |
Cat#304822 |
| PerCP/Cyanine5.5 anti-human CD197 (CCR7) Antibody (Clone: G043H7) |
Biolegend |
Cat#353219 |
| APC anti-human CD127 (IL-7Rα) Antibody (Clone: A019D5) |
Biolegend |
Cat#351315 |
| FITC anti-human CD183 (CXCR3) Antibody (Clone: G025H7) |
Biolegend |
Cat#353703 |
| EOMES Monoclonal Antibody (WD1928), PECyanine7 |
eBioscience™ |
Cat#25–4877–42 |
| APC anti-T-bet Antibody (Clone: 4B10) |
Biolegend |
Cat#644813 |
| PE anti-TCF1 (TCF7) Antibody (Clone: 7F11A10 ) |
Biolegend |
Cat#655207 |
| FITC anti-human/mouse Bcl-6 Antibody (Clone: 7D1) |
Biolegend |
Cat#358513 |
| APC anti-human Notch 1 Antibody (Clone: MHN1–519 ) |
Biolegend |
Cat#352107 |
| PerCP/Cyanine5.5 anti-GATA3 Antibody (Clone: 16E10A23) |
Biolegend |
Cat#653811 |
| RUNX1 Monoclonal Antibody (RXDMC), PE |
eBioscience™ |
Cat#12–9816–80 |
| Anti-human CTLA4 (CD152)-161Dy |
FLUIDIGM |
Cat#3161004B |
| Anti-human TIM3–153Eu |
Yale CyTOF CORE |
|
| Anti-human CD278/ICOS-168Er |
FLUIDIGM |
Cat#3168024B |
| Anti-human TNFRSF9/CD137–173Yb |
FLUIDIGM |
Cat#3173015B |
| Anti-human IL2–166Er |
FLUIDIGM |
Cat#3158007B |
| Anti-human TNF-α-152Sm |
FLUIDIGM |
Cat#3152001B |
| Anti-human IFN-γ-165Ho |
FLUIDIGM |
Cat#3165002B |
| Anti-human CXCR3–163Dy |
FLUIDIGM |
Cat#3163004B |
| Anti-human CD62L-174Yb |
Yale CYTOF Core |
Cat#V00751
|
| Anti-human Perforin-176Yb |
Yale CYTOF Core |
|
| Anti-human CD45RA-169Tm |
FLUIDIGM |
Cat#3143006B |
| Anti-human CD8a-146Nd |
FLUIDIGM |
Cat#3146001B |
| Anti-human CD45RO-164Dy |
FLUIDIGM |
Cat#3164007B |
| Anti-human CD3–170Er |
FLUIDIGM |
Cat#3170001B |
| Anti-human CD45–89Y |
FLUIDIGM |
Cat#3089003B |
| Anti-Cleaved Caspase3–172Yb |
Yale CYTOF Core |
|
| Anti-human CD25–149Sm |
FLUIDIGM |
Cat#3149010B |
| Anti-human CD134(OX40)-150Nd |
Yale CYTOF Core |
|
| Anti-human LAG3–175Lu |
Yale CYTOF Core |
|
| Recombinant Human Siglec-2/CD22 Fc Chimera Protein, CF |
R&D |
Cat#1968-SL-050 |
| Recombinant Human BCMA/TNFRSF17 Fc Chimera Protein, CF |
R&D |
Cat#193-BC-050 |
| Dynabeads Human T-Activator CD3/CD28 |
Invitrogen |
Cat#11131D |
| Anti-human PRODH2 |
Atlas Antibodies |
Cat#HPA051287 |
| Anti-human Vinculin |
Abcam |
Cat#129002 |
| Bacterial and Virus Strains |
|
|
| One Shot Stbl3 Chemical Competent E. coli |
ThermoFisher |
Cat#C737303 |
| Endura™ ElectroCompetent Cells |
Lucigen |
Cat#60242–2 |
|
|
|
| Biological Samples |
|
|
|
|
|
|
|
|
| Chemicals, Peptides, and Recombinant Proteins |
|
|
| PEI MAX -Transfection Grade Linear Polyethylenimine Hydrochloride (MW 40,000) |
Polyscience |
Cat#24765–1 |
| DPBS, no calcium, no magnesium |
Gibco |
Cat#14190136 |
| RPMI 1640 Medium |
Gibco |
Cat#11875–093 |
| Fetal Bovine Serum |
Sigma Aldrich |
Cat#F4135–500ML |
| DMEM, high glucose, pyruvate |
Gibco |
Cat#11995065 |
| Opti-MEM™ I Reduced Serum Medium |
ThermoFisher |
Cat#31985070 |
| Penicillin-Streptomycin (10,000 U/mL) |
Gibco |
Cat#15140122 |
| Lonza™ BioWhittaker™ L-Glutamine (200mM) |
Lonza |
Cat#BW17605E |
| 2-Mercaptoethanol |
Sigma Aldrich |
Cat#M6250–10ML |
| X-VIVO 15 Serum-free Hematopoietic Cell Medium |
Lonza |
Cat#BE02–060F |
| Human AB Serum; Male Donors; type AB |
MP Biomedical |
Cat#092930949 |
| ACK Lysing Buffer |
Lonza |
Cat#10–548E |
| Naïve CD8a+ T Cell Isolation Kit, mouse |
Miltenyi |
Cat#130–096-543 |
| LS Columns |
Miltenyi |
Cat#130–042-401 |
| Recombinant Mouse IL-2 (carrier-free) |
Biolegend |
Cat#575404 |
| Recombinant Mouse IL-7 (carrier-free) |
Biolegend |
Cat#577802 |
| Recombinant Mouse IL-12 (p70) (carrier-free) |
Biolegend |
Cat#577008 |
| Recombinant Mouse IL-15 (carrier-free) |
Biolegend |
Cat#566302 |
| Recombinant Human IL-2 (carrier-free) |
Biolegend |
Cat#589104 |
| Monensin Solution (1,000x) |
Biolegend |
Cat#420701 |
| Brefeldin A Solution (1,000X) |
Biolegend |
Cat#420601 |
| QuickExtract DNA Extraction Solution |
Epicenter |
Cat#QE09050 |
| Proteinase K |
Qiagen |
Cat#19131 |
| Pierce™ Universal Nuclease for Cell Lysis |
ThermoFisher |
Cat#88702 |
| RNase A |
Qiagen |
Cat#19101 |
| PEG 8000, Molecular Biology Grade |
Promega |
Cat#V3011 |
| Sodium chloride |
Sigma |
Cat#S3014 |
| Gibson Assembly® Master Mix |
NEB |
Cat#E2611 |
| Phusion Flash High-Fidelity PCR Master Mix |
ThermoFisher |
Cat#F548L |
| DreamTaq Green PCR Master Mix (2X) |
ThermoFisher |
Cat#K1082 |
| E-Gel™ Low Range Quantitative DNA Ladder |
ThermoFisher |
Cat#12373031 |
| Fixation/Permeabilization Solution Kit |
BD |
Cat#554714 |
| SuperScript™ IV Reverse Transcriptase |
Invitrogen |
Cat#18090050 |
| Random Hexamers (50 μM) |
Invitrogen |
Cat#N8080127 |
| NEBNext® Ultra™ RNA Library Prep Kit for Illumina® |
NEB |
Cat#E7530S |
| NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) |
NEB |
Cat#E7335S |
| TaqMan™ Fast Advanced Master Mix |
Invitrogen |
Cat#4444557 |
| QIAquick Gel Extraction Kit |
Qiagen |
Cat#28706 |
| QIAamp Fast DNA Tissue Kit |
Qiagen |
Cat#51404 |
| EndoFree® Plasmid Maxi Kit |
Qiagen |
Cat#12362 |
| RNeasy Mini Kit |
Qiagen |
Cat#74104 |
| Relative Human Mitochondrial DNA Copy Number Quantification qPCR Assay Kit |
ScienCell |
Catalog#8938 |
| Human IL-2 ELISA Kit |
Millipore Sigma |
Cat#RAB0286 |
| IL-7 Human ELISA Kit |
ThermoFisher |
Catalog#EHIL7 |
| IL-15 Human ELISA Kit |
ThermoFisher |
Catalog#BMS2106 |
| Agilent Seahorse XF Cell Mito Stress Test Kit |
Agilent |
Cat#103015–100 |
| Agilent Seahorse XF Calibrant solution |
Agilent |
Cat#100840–000 |
| Agilent Seahorse XF RPMI medium |
Agilent |
Cat#103576–100 |
| Agilent Seahorse XF sensor cartridges and cell culture microplates |
Agilent |
Cat#101085–004 |
| Poly-D-lysine |
Sigma |
Cat#27964–99–4 |
| Seahorse XF 100 mM Pyruvate Solution |
Agilent |
Cat#103578–100 |
| Seahorse XF 1.0 M Glucose Solution |
Agilent |
Cat#103577–100 |
| Seahorse XF 200 mM Glutamine Solution |
Agilent |
Cat#103579–100 |
| Bovine Serum Albumin |
Sigma Aldrich |
Cat#A9418–100G |
| EDTA |
Sigma Aldrich |
Cat#E8008–100ML |
| XenoLight D-Luciferin – K+ Salt Bioluminescent Substrate |
Perkin Elmer |
Cat#122799 |
| Neon™ Transfection System 100 μL Kit |
Invitrogen |
Cat#MPK10025 |
| HiFi Cas9 protein |
IDT |
Cat#1081061 |
| Cas9 tracrRNA |
IDT |
Cat#1072532 |
| crRNA |
IDT |
Custom, sequence specific |
| Standard metabolites list |
Sigma |
Table S6 |
| OVA 257–264 |
Invivogen |
Cat#vac-sin |
| BpiI (BbsI) (10 U/μL) |
ThermoFisher |
Cat#ER1012 |
| Esp3I (BsmBI) (10 U/μL) |
ThermoFisher |
Cat#ER0451 |
| 4-Hydroxyproline |
Sigma |
Cat#H54409
|
| Acetyl CoA |
Sigma |
Cat#A2056 |
| ADP |
Sigma |
Cat#A2754 |
| Amino acid standards, physiological |
Sigma |
Cat#A9906 |
| AMP |
Sigma |
Cat#1930 |
| Arginine |
Sigma |
Cat#A5006 |
| ATP |
Sigma |
Cat#A26209
|
| cAMP |
Sigma |
Cat#A9501 |
| Choline |
Sigma |
Cat#C7017 |
| CoA |
Sigma |
Cat#C4282 |
| CTP |
Sigma |
Cat#C1506 |
| Fumarate |
Sigma |
Cat#D95654 |
| Glucose |
Sigma |
Cat#G8270 |
| Glutathione |
Sigma |
Cat#G4251 |
| Glyceraldehyde3P |
Sigma |
Cat#G5251 |
| Glycerate3P |
Sigma |
Cat#P8877 |
| Glyoxylate |
Sigma |
Cat#G4502 |
| GTP |
Sigma |
Cat#G8877 |
| IMP |
Sigma |
Cat#I4625 |
| Malate |
Sigma |
Cat#46940 |
| Myo-Inositol |
Sigma |
Cat#I5125 |
| Orinithine |
Sigma |
Cat#57197 |
| Oxaloacetate |
Sigma |
Cat#O4216 |
| Palmitoyl CoA |
Sigma |
Cat#P9716 |
| Proline |
Sigma |
Cat#P3350000 |
| PRPP |
Sigma |
Cat#P8296 |
| Putrescine |
Sigma |
Cat#51799 |
| Pyruvate |
Sigma |
Cat#P2256 |
| Ribose5P |
Sigma |
Cat#83875 |
| Spermidine |
Sigma |
Cat#S2626 |
| Spermine |
Sigma |
Cat#S3256 |
| Sphingosine |
Sigma |
Cat#S7049 |
| Succinate |
Sigma |
Cat#W327700 |
| Tetrahydrofolic acid |
Sigma |
Cat#G5251 |
| TTP |
Sigma |
Cat#T0251 |
| UTP |
Sigma |
Cat#U6375 |
| Xylose-5-Phosphase |
Sigma |
Cat#78963 |
| α-Hydroxyglutaric acid |
Sigma |
Cat#90790 |
|
|
|
| Critical Commercial Assays |
|
|
|
|
|
| Deposited Data |
|
|
| human CAR-T cell RNA-seq |
This paper |
PRJNA806391 |
| human CD8 T cell metabolomics |
This paper |
ST002085 |
| human CAR-T cell metabolomics |
This paper |
ST002084 |
| CyTOF data |
This paper |
DOI: 10.17632/pnbjdtdkfg.1 |
|
|
|
| Experimental Models: Cell Lines |
|
|
| HEK293FT |
ThermoFisher |
Catalog Number: R70007
|
| HEK293T |
ATCC |
Catalog Number: CRL-3216™
|
| NALM6 |
ATCC |
Catalog Number:3273 |
| MCF-7 |
ATCC |
Catalog Number: HTB-22 |
| E0771 |
CH3 |
Catalog Number: 940001 |
| MB-MDA-231 |
ATCC |
Catalog Number: HTB-26 |
| MM.1R |
ATCC |
Catalog Number:CRL-2975 |
| Human Peripheral Blood CD8+ T Cells |
STEMCELL |
Catalog Number: 70027 |
| Human Peripheral Blood Mononuclear Cells |
STEMCELL |
Catalog Number: 70025.1 |
|
|
|
| Experimental Models: Organisms/Strains |
|
|
| OT-I |
Jackson Laboratory |
Stock No: 003831 |
| NSG |
Jackson Laboratory |
Stock No: 005557 |
| Cas9ß |
Platt et al., 2014
|
Jackson Lab |
| OT-I;Cas9ß |
Dong et al. 2019 Cell |
Sidi Chen lab |
|
|
|
| Oligonucleotides |
|
|
| mm10dg library |
This paper |
Dataset S1 |
| Taqman probes |
This paper |
Table S3 |
| Amplicon primers for surveyor or Nextera |
This paper |
Table S2 |
| gBlocks of U6-dgRNA-MS2 |
IDT |
Custom, sequence specific |
| EFS-Thy1.1-MCP-p65-HSF1 |
IDT |
Custom, sequence specific |
| Prodh2 probe |
ThermoFisher |
Mm00457662-m1 |
| Actb probe |
ThermoFisher |
Mm00607939-s1 |
| Gapdh probe |
ThermoFisher |
Mm99999915_g1 |
| Wdr37 probe |
ThermoFisher |
Mm00552518-m1 |
| Srek1ip1 probe |
ThermoFisher |
Mm00482686-m1 |
| Ccnb1ip1 probe |
ThermoFisher |
Rn01414585-m1 |
| PRODH2 probe |
ThermoFisher |
Hs00560411-m1 |
| ACTB probe |
ThermoFisher |
Hs99999903-m1 |
| GAPDH probe |
ThermoFisher |
Hs02786624-g1 |
|
|
|
| Recombinant DNA |
|
|
| psPAX2 |
Addgene |
Cat#12260 |
| pMD2.G |
Addgene |
Cat#12259 |
| pRepCap6 (AAV6 capsid) |
Addgene |
Cat#110770 |
| pAdDeltaF6 (PDF6) |
Addgene |
Cat#112867 |
| TdgA Vector |
This study |
Sidi Chen lab |
| Mm10dgLib library |
This study |
Sidi Chen lab |
|
|
|
| Software and Algorithms |
|
|
| FlowJo software 9.9.6 |
FlowJo, LLC |
https://www.flowjo.com
|
| Cutadapt |
Martin et al., 2011
|
https://cutadapt.readthedocs.io/en/stable/
|
| DAVID |
Huang et al., 2009
|
https://david.ncifcrf.gov
|
| Scran R package |
Lun et al., 2016 |
https://www.r-project.org
|
| Rtsne R package |
Maaten, 2014; Maaten and Hinton, 2008 |
https://www.r-project.org
|
| Edge R package |
Robinson et al., 2010 |
https://www.r-project.org
|
| Kallisto |
Bray et al., 2016
|
https://pachterlab.github.io/kallisto/
|
| Sleuth |
Pimentel et al., 2017
|
https://pachterlab.github.io/sleuth/
|
| GSEA |
Subramanian et al., 2005
|
http://software.broadinstitute.org/gsea/index.jsp
|
| PSCAN |
Zambelli et al., 2009 |
http://159.149.160.88/pscan/
|
| Bowtie 1.1.2 |
Langmead et al., 2009
|
http://bowtiebio.sourceforge.net
|
| Agilent Mass Hunter Qualitative Analysis Software |
Agilent |
(Version B.07.0.0, build 7.0.7024.0). |
| Agilent Mass Profiler Professional |
Agilent |
(Version 14.5-Build 2772) |
| Metabolite database |
HMDB |
http://www.hmdb.ca/
|
| Metabolite database |
METLIN |
http://metlin.scripps.edu
|
| MetaboAnalyst 4.0 |
Chong et al., 2018; Xia et al., 2015
|
https://www.metaboanalyst.ca
|
| Pathvisio v3.3.0 |
Pathvisio |
https://www.pathvisio.org
|
| KEGG |
KEGG |
http://www.genome.jp/kegg/
|
|
|
|
| Other |
|
|
|
|
|
|
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