REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rat anti-mouse CD4 clone GK1.5 or RM4-5	Biolegend	Cat#100423, 100532
Rat anti-mouse/human CD44 clone IM7	Biolegend	Cat#103032, 103008
Rat anti-mouse CD62L clone MEL-14	Biolegend	Cat#104412
Armenian Hamster anti-mouse CD69 clone H1.2F3	Biolegend	Cat#104537
Rat anti-mouse CD25 clone PC61	Biolegend	Cat#102016
Mouse anti-mouse Tbet clone 4B10	Biolegend	Cat#644810
Rat anti-mouse IFNγ clone XMG1.2	Biolegend	Cat#505813
Rat anti-mouse IL-17a clone TC11-18H10.1	Biolegend	Cat#506904
Mouse anti-mouse Rorγt clone Q31-378	BD BioScience	Cat#562684
Rat anti-mouse Foxp3 clone FJK-16s	eBioscience	Cat#17-5773-82
Armenian Hamster anti-mouse Fas (CD95) clone Jo2	BD BioScience	Cat#554257
Rat anti-mouse anti-GL-7 clone GL7	Biolegend	Cat#144612, 144610
Mouse anti-mouse anti-Bcl-6 clone K112-91	BD BioScience	Cat#561522
Armenian Hamster anti-mouse anti-ICOS (CD278) clone C398.4A	Biolegend	Cat#313525
Rat anti-mouse CXCR5 (CD185) clone SPRCL5	Biolegend	Cat#145513
Rat anti-mouse PD-1 (CD279) clone 29F.1A12	Biolegend	Cat#135216
Rat anti-mouse B220 clone RA3-6B2	Biolegend, Tonbo	Cat#103229, 20-0452-U100
Rat anti-mouse CD19 clone 1D3	Biolegend	Cat#115555, 115522
Armenian Hamster anti-mouse CD3e clone 145-2C11	Biolegend	Cat#100319, 100309
Rat anti-mouse anti-IL-2 clone JES6-5H4	Biolegend	Cat#503808
Rat anti-mouse Vα2 clone B20.1	Biolegend,	Cat#127816
Armenian Hamster anti-mouse anti-Vβ8.3 clone 1B3.3	BD BioScience	Cat#553664
Armenian Hamster anti-mouse CD3 clone 2C11 (for coating)	BioXcell	Cat#BP0001-1
Armenian Hamster anti-mouse CD28 clone PV-1 (for coating)	BioXcell	Cat#BE0015-5
Rat anti-mouse CD16/CD32 clone 2.4G2 (for blocking)	BioXcell	Cat#BE0307
anti-IL4 clone 11B11	UCSF	AM039-PURE-B25
anti-IFNγ clone XMG1.2	UCSF	AM034-PURE-B25
anti-IL12/23 clone C17.8	UCSF	AM037-PURE-B25
Goat anti-mouse IgG1	ThermoFisher	A21240
Mouse anti-mouse NFATC2 clone 25A10.D6.D2	ThermoFisher	MA1-025
Bacterial and virus strains
LCMV Armstrong	Annaise Jauch	N/A
Chemicals, peptides, and recombinant proteins
FCS for medium	Atlanta	S11150
HEPES	SIGMA	H0887
Sodium pyruvate	Gibco	11360-039
non-essential amino acids	Gibco	11140-050
Glutamax	Gibco	35050-038
0.1% 2-Mercaptoethanol	Gibco	31350-010
FCS for FACS buffer	Milian	S0750
NaN3	SIGMA	S2002-5G
NH4Cl	SIGMA	A9434-500G
NaHCO3	SIGMA	S5761-500G
Proteinase K	Promega	V3021
TE buffer	SIGMA	93283-100ML
Fixation/Permeabilization Concentrate	invitrogen	00-5123-43
Fixation/Permeabilization Diluent	invitrogen	00-5223-5
Permeabilization Buffer 10X	eBioscience	00-8333-56
OneComp eBeads	invitrogen	01-111-42
TRI Reagent	Sigma-Aldrich	T9424-200ML
1-Bromo-3-chloropropane	Sigma-Aldrich	B9673-200ML
M-MLV Reverse Transcriptase	Sigma-Aldrich	M1302-40KU
TaqMan™ MicroRNA Reverse Transcription Kit	ThermoFisher	4366597
TaqMan™ Fast Universal PCR Master Mix (2X), no AmpErase™ UNG	ThermoFisher	4364103
TaqMan Gene Expression Assays RCAN3	ThermoFisher	4351372
TaqMan Gene Expression Assays 18S	ThermoFisher	4331182
MicroAmp™ Fast Optical 96-Well Reaction Plate, 0.1 mL	ThermoFisher	4346907
EasySep naïve CD4+ T cell Isolation Kit	STEMCELL	19765A
CellTAK adhesive	Corning	354241
Seahorse XFe96/XF96 FluxPak (18 cartr.)	SeahorseBiotech	PN 102416-100
Glucose-free unbuffered RPMI	SIGMA	R6504-10X1L
Oligomycin	SIGMA	495445
FCCP	SIGMA	C2920
Rotenone	SIGMA	R8875
D-(+)-Glucose	Sigma-Aldrich	G7021
Fixable Viability Dye eF780	eBioscience	65-0865-14
Cell Trace Violet (CTV)	ThermoFisher	C34557
Phorbol 12-Myristate 13-Acetate (PMA)	Sigma	P1585
Ionomycin	Sigma	10634-1MG
Brefeldin A (BFA)	Sigma	B7651-5MG
GP-64	Neosystem	SP991567B
IL-2	R&D	202-IL
Retinoic acid	Sigma	R2625
rhTGFβ	R&D	P01137
IL-6	R&D	406ML
IL-7	R&D	407-ML-005
Cyclosporin A (CsA)	Sigma	30024
DAPI	Sigma	10236276001
IL-12	R&D	419ML
TMB	BD	555214
Cas9 nuclease	QB3 MacroLab, UC Berkeley	N/A
Sodium deoxycholate	Thermo Scientific	89904
TRIS	Sigma,	T6791
TCEP	Sigma	646547-10x1ml
PR-Sulfonate Cartridges	PreOmics	N/A
Microplate BCA Protein Assay Kit	Thermo-Pierce	23252
Chloroacetamide	Sigma	C0267-100G
TFA	Pierce/Thermo	28904
Lysin-C	Wako	125-05061
Porcine Trypsin	Promega	V5113
2-Propanol	Sigma-Aldrich	I9516-500ML
Ethanol	Sigma-Aldrich	51976-500ML-F
Ammonium hydroxide solution	Sigma-Aldrich	17093-1L
HPLC water	Chemie Brunswick	W/0106/17
Acetonitrile	Thermo Scientific	A955-212
Formic acid	Sigma	94318-50ml
Poly-L-glutamic acid sodium salt (PGA)	Sigma	P4761
QuickExtract	Lucigen	QE09050
Critical commercial assays
ELISA MAX mouse IL-2 set	BioLegend	431002
Nunc-Immuno™ MicroWell™ 96 well solid plates	SIGMA	M9410-1CS
Zymol Directzol kit	ZymoResearch	R2060
Deposited data
Raw and analyzed data	This paper	N/A
Mouse reference genome	UCSC	MM10
Generated data GEO accession number	This paper	GSE140568
Experimental models: Organisms/strains
Mir17-92<tm1.1Tyj>/J (crossed to CD4cre, T1792Δ/Δ)	Dr. Bluestone, UCSF	N/A
C57Bl/6-Gt(ROSA)26Sor<tm3(CAG-MIRN17-92,-EGFP)Rsky>/J (crossed to CD4cre, T1792tg/tg)	The Jackson Laboratory	stock number 008517
B6.Cg-Tg(Cd4-cre)1Cwi/BfluJ	The Jackson Laboratory	stock number 022071
B6.129S2-Cd28tm1Mak/J	SWIMR	N/A
B6-Tg(TCRGP13)1 Brl	SWIMR	N/A
Oligonucleotides
Rcan3 crRNA GAGAAATACGAACTGCACGC	IDT	N/A
Cyld crRNA GTTGGCAATTACCAACTGTG	IDT	N/A
Pten crRNA CCTCCAATTCAGGACCCACG	IDT	N/A
Phlpp2 crRNA TTGTACACTGCAGCAGACGA	IDT	N/A
Nrbp1 crRNA AAACTGCTTAAGACTCCCAG	IDT	N/A
Rnf38 crRNA CTCCTACACGGTAACTACGG	IDT	N/A
Rnf167 crRNA GGAATGAGGTAATAGCCCAA	IDT	N/A
Negative control crRNA#2	IDT	1072545
tracrRNA	IDT	1072532
fwd primer Rcan3 TCAGCCACTGAATGACGTAGTAG	Microsynth	N/A
rev primer Rcan3 GCGTCTGCGTGATTTTCTGT	Microsynth	N/A
Fwd primer Cyld CCTGTGGAGCCAAGAGAAAGT	Microsynth	N/A
Rev primer Cyld TCCTGGGGTCTATCCTGAGAA	Microsynth	N/A
Fwd primer Pten AGAAGTCCTTACATGGGTTGGT	Microsynth	N/A
Rev primer Pten GCTTTAAGCAAAAGGTCTGTGGT	Microsynth	N/A
Fwd primer Phlpp2 GTGTCTGCCCTGGCTATGGA	Microsynth	N/A
Rev primer Phlpp2 GTGGTCCAGGAAGGAGTAACAG	Microsynth	N/A
Fwd primer Nrbp1 GTTCTCACTGTGCTCTTAAGCC	Microsynth	N/A
Rev primer Nrbp1 CCCACTAGTCCTTGCTATCCC	Microsynth	N/A
Fwd primer Rnf38 TACTTGAGCTACCTCCCCCG	Microsynth	N/A
Rev primer Rnf38 TCAGTTGGAAGTGAAGCTACAAA	Microsynth	N/A
Fwd primer Rnf167 AAGCGCAGAGTACCTACGAG	Microsynth	N/A
Rev primer Rnf167 TCCCCTCTACCGATCCAGTC	Microsynth	N/A
Software and algorithms
FlowJo 10.6.0	BD	N/A
Prism 8.2.0	GraphPad	N/A
IDEAS software v6.2	Merck	N/A
TIDE	Brinkman et al. (2014)	https://tide.nki.nl/
Fragment Analyzer	Advanced Analytical	N/A
FastQC tool version 0.11.5	Andrews (2010)	N/A
STAR version 2.5.2a	Dobin et al. (2013)	N/A
R software version 3.5	R Core Team 2015	http://www.R-project.org/
R Bioconductor package QuasR version 1.18	Gaidatzis et al., 2015b	N/A
R Bioconductor package edgeR version 3.24.3	Robinson et al. (2010)	N/A
ImageJ	Schneider et al. (2012)	https://imagej.nih.gov/ij/
Other
Sequence data, analyses, and resources related to the RNA-sequencing of T1792Δ/Δ, wt, T1792tg/tg	This paper	N/A
Sequence data, analyses, and resources related to the RNA-sequencing of CD28−/−, rescue, T1792Δ/Δ, wt, T1792tg/tg	This paper	N/A
Curated gene set collection of the Molecular Signature Database (MSigDB v6.0)	Subramanian et al. (2005)	N/A