REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
BCL-2 PE/Cy7	BioLegend	RRID: AB_2565247
BCL-6 AF647	BD Biosciences	RRID: AB_10898007
CD3e	BD Biosciences	RRID: AB_394590
CD4 AF700	Thermo Fisher	RRID: AB_493999
CD4 APC	BioLegend	RRID: AB_312719
CD4 eF450	Thermo Fisher	RRID: AB_10718983
CD4 FITC	BD Biosciences	RRID: AB_394583
CD16/CD32	BD Biosciences	RRID: AB_394655
CD28 biotin	Thermo Fisher	RRID; AB_466411
CD28	BD Biosciences	RRID: AB_394763
CD44 PE	BioLegend	RRID: AB_312959
CD48 FITC	Thermo Fisher	RRID: AB_465076
CD69PE/Cy7	BioLegend	RRID: AB_493564
CD84 PE	BioLegend	RRID: AB_2074757
CD95 biotin	BD Biosciences	RRID: AB_395328
CD122 PE	Thermo Fisher	RRID: AB_465832
CD134 APC	Thermo Fisher	RRID: AB_10717260
CD150 PE/Cy7	BioLegend	RRID: AB_439796
CD152 APC	BioLegend	RRID: AB_2087653
CD153 biotin	Thermo Fisher	RRID: AB_466622
CD162 AF647	BD Biosciences	RRID: AB_2737807
CD183 BV421	BioLegend	RRID: AB_2563100
CD185	BD Biosciences	RRID: AB_394302
CD197 PE	BioLegend	RRID: AB_389357
CD229 PE	BioLegend	RRID: AB_2137958
CD244.2 PE/Cy7	Thermo Fisher	RRID: AB_257343
CD267 APC	Thermo Fisher	RRID: AB_842759
CD278 PE	BD Biosciences	RRID: AB_394349
CD279 eF450	Thermo Fisher	RRID: AB_11150068
CD279 PE/Cy7	Thermo Fisher	RRID: AB_10853805
GATA3 PE/Cy7	Thermo Fisher	RRID: AB_2573568
IFN-y Pacific blues	BioLegend	RRID: AB_893526
IFN-y	Bio X cell	RRID: AB_1107694
IFN-yR1	Thermo Fisher	RRID: AB_2573097
IL-10R PE	BioLegend	RRID: AB_313518
IL-21R APC	BioLegend	RRID: AB_2295868
IL-23R PE	BioLegend	RRID: AB_2572188
IL-2	BioLegend	RRID: AB_315292
IL-4	Bio X cell	RRID: AB_1107707
IRF4 eF660	Thermo Fisher	RRID: AB_2574393
Ly108 PE	Thermo Fisher	RRID: AB_763616
Nur77 PE	Thermo Fisher	RRID: AB_1257210
p4E-BP1 AF647	Cell Signaling	RRID: AB_2097838
pAKT PE/Cy7	Thermo Fisher	RRID: AB_2688172
pS6 Pacific blue	Cell Signaling	RRID: AB_2797646
RORyT BV421	BD Biosciences	RRID: AB_2687545
T-bet eF450	Thermo Fisher	RRID: AB_2784726
TGF-β	R&D Systems	RRID: AB_357931
Anti-rabbit IgG HRP	Cell Signaling	RRID: AB_2099233
Anti-mouse IgG HRP	Cell Signaling	RRID: AB_330924
H3K36me2 Ab	Cell Signaling	RRID: AB_1030983
Histone 3 Ab	Cell Signaling	RRID: AB_2756816
Chemicals, peptides, and recombinant proteins
Fixable viability dye	Thermo Fisher	65-0865
MitoSOXTM Red	Thermo Fisher	M36008
CM-H2DCFDA	Thermo Fisher	C6827
MitoTracker® Red CMXRos	Thermo Fisher	M7512
MitoTracker™ Deep Red	Thermo Fisher	M22426
2-NBDG	Thermo Fisher	N13195
BODIPY	Thermo Fisher	D3823
Duramycin-LC	Molecular Targeting Technologies	D-1003
Streptavidin PE/Cy7	BD Biosciences	557598
Streptavidin BV650	BioLegend	405231
Streptavidin PerCP	BD Biosciences	554064
dsDNA	Sigma	D8515
p-nitrophenol phosphate (PNPP) substrate	Thermo Fisher	34045
4 - 20% SDS-PAGE gels	Bio-Rad	4561094
Western ECL substrate	Cell Signaling	6883S
AMPure XP beads	Beckman Coulter	A63880
Restore™ Western Blot Stripping Buffer	Thermo Fisher	21059
Foxp3 / Transcription Factor Staining Buffer Set	Thermo Fisher	00-5523-00
cell signaling lysis buffer	Sigma	43-040
protease inhibitor cocktail	Sigma	S8820-20
SYBR® Green Supermix	Bio-Rad	1725271
RPMI-1640	Corning	10-040-CV
IL-6	Shenandoah Biotech	200-02
IL-21	Pepro Tech	210-21
Activin A	Thermo Fisher	PHC9564
Critical commercial assays
RNeasy Kit	Qiagen	74004
TruSeq Stranded RNA Sample Preparation Kit	Illumina	20020597
PicoGreen assay	Thermo Fisher	P7589
CD4 T Cell Isolation Kit	Miltenyi Biotec	130-104-454
Naïve CD4 T Cell Isolation Kit	Miltenyi Biotec	130-104-453
BCA protein assay kit	Pierce	23225
Impromptu-II™ Reverse Transcription System	Promega	A3800
Deposited data
Raw RNA-seq data	GEO	GSE 157648
Oher raw and processed data	Github	https://github.com/gmhhope/TC_TFH_omics_analysis/.
Analysis workflows		https://github.com/gmhhope/TC_TFH_omics_analysis/.
Experimental models: Organisms/strains
B6.NZM-Sle1NZM2410/AegSle2NZM2410/AegSle3NZM2410/Aeg/LmoJ (TC) female mice	In house and Jackson laboratories	# 007228
C57BL6/J female mice	Jackson laboratories	#000664
Oligonucleotides
Smyd2 F	N/A	F: 5′-AAGGATTGTCAAAATGTGGACGG-3′
Smyd2 R	N/A	R: 5′-ATGGAGGAGCATTCCAGCTTG-3′
Hsp90 F	N/A	F: 5′-GTCCGCCGTGTGTTCATCAT-3′
Hsp90 R	N/A	R: 5′-GCACTTCTTGACGATGTTCTTGC-3′
Software and algorithms
FlowJo V10	Tree Star	https://www.flowjo.com/solutions/flowjo/downloads
Prism 9.0	Graphpad	https://www.graphpad.com/scientific-software/prism/
ImageJ	NIH	https://imagej.nih.gov/ij/
STAR aligner v2.785	N/A	https://github.com/alexdobin/STAR
FeatureCounts (v2.0)	N/A	https://subread.sourceforge.net/featureCounts.html
DESeq	N/A	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
pheatmap R function (version 1.0.12)	N/A	https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12/topics/pheatmap
Matplotlib-Venn (Version 0.11.5)	N/A	https://packages.ubuntu.com/bionic/python-matplotlib-venn
javaGSEA (v3.0)	N/A	https://www.gsea-msigdb.org/gsea/index.jsp
Molecular Signature Database (MSigDB v5.2)	N/A	https://www.gsea-msigdb.org/gsea/msigdb/
R function Dotplot in Lattice package (version 0.3-1)	N/A	https://www.rdocumentation.org/packages/lattice/versions/0.3-1/topics/dotplot
Metamorph software	Molecular Devices	https://www.moleculardevices.com/products/cellular-imaging-systems/acquisition-and-analysis-software/metamorph-microscopy
Others
ACE 18-PFP 100 x 2.1 mm, 2 μm column	Mac-Mod Analytical	N/A
LSRFortessa	BD Biosciences	N/A
FACSAria III	BD Biosciences	N/A