REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies and dyes
Brilliant Violet 510™ anti-human CD69 Antibody	Biolegend	Cat#310936 RRID:AB_2563834
APC anti-human CD69 Antibody	Biolegend	Cat# 310910 RRID:AB_314845
Zombie NIR™ Fixable Viability Kit	Biolegend	Cat# 423106
H3K27Ac antibody	Active Motif	Cat# 39133 RRID:AB_2561016
H3K27Me3 antibody	Active Motif	Cat# 39155 RRID:AB_2561020
GATA-3 (D13C9) XP Rabbit mAb	Cell Signaling Technology	Cat# 5852, RRID:AB_10835690
Dec1 antibody	Novus Biologicals	Cat#NB100-1800
TAL1 antibody	SantaCruz Biotech	Cat#sc-393287
Cell lines and primary cells
Jurkat cell line, Clone E6.1	ATCC	Cat#TIB152, RRID:CVCL_0367
CD4+ T cells	AllCells	N/A
Chemicals and buffers
Phorbol 12-myristate 13-acetate	Sigma-Alrich	Cat#P8139
Ionomycin calcium salt	Sigma-Alrich	Cat# I0634
Chloroquine diphosphate	Millipore Sigma	Cat#C6628
Polybrene	Sigma-Alrich	Cat#107689
Brilliant Staining Buffer	BD	Cat#566349
Recombinant DNA
KRAB-dCas9-sgRNA-Puro	Broad GPP	pXPR_066
LentiCRISPR v2-dCas9	Addgene	Cat#112233 RRID:Addgene_112233
rApobec-nCas9-UGI-Puro	Broad GPP	pRDA_256
EFS-ABE8e-V106W-nCas9-puro	Broad GPP	pRDA_426
GATA3-Overexpression-GFP	In this study	N/A
BHLHE40-Overexpression-GFP	In this study	N/A
BHLHE41-Overexpression-GFP	OriGene	Cat#: RC206882L2
sgCtrl-1 CRISPR-Cas9-GFP	In this study	sgRNA sequence: GGCTAAATTCCTCTTATTCA
sgCtrl-2 CRISPR-Cas9-GFP	In this study	sgRNA sequence: GTAACCAAGAGTCAGGACTG
sgGATA3-1 CRISPR-Cas9-GFP	In this study	sgRNA sequence: ACCGAGTTTCCGTAGTAGGG
sgGATA3-2 CRISPR-Cas9-GFP	In this study	sgRNA sequence: TACGTGCCCGAGTACAGCTC
shCtrl(Scamble shRNA-EGFP)	VectorBuilder	Target sequence:CCTAAGGTTAAGTCGCCCTCG
shBHLHE40-1(EGFP)	VectorBuilder	Target sequence: AGAAAGGATCGGCGCAATTAA
shBHLHE40-2(EGFP)	VectorBuilder	Target sequence: ACCCGAACATCTCAAACTTAC
TAL1-Overexpression-Puro	OriGene	Cat#RC222628L3
pLenti-Overexpression-Puro	OriGene	Cat#PS100092
psPAX2	Addgene	Cat#12260 RRID:Addgene_12260
pMD2.G	Addgene	Cat#12259 RRID:Addgene_12259
Lentivirus packing
Lipofectamine 3000 Transfection Reagent	ThermoFisher	Cat#L3000001
OptiMEM	ThermoFisher	Cat# 31985070
ATAC-seq reagents
Illumina tagmentation kit	Illumina	Cat#20034197
Nextera XT Index Kit	Illumina	Cat# FC-131-1001
MinElute Reaction Purification Kit	QIAGEN	Cat#28003
MinElute PCR Purification Kit	QIAGEN	Cat#28004
NEBNext High-Fidelity 2X PCR Master Mix	NEB	Cat# M0541
RNA-seq reagents
QIAGEN RNeasy Micro kit	QIAGEN	Cat# 74004
Dynabeads mRNA Direct Kit	ThermoFisher	Cat# 610.12
RNA Fragmentation Reagents	ThermoFisher	Cat# AM8740
Turbo DNase	ThermoFisher	Cat#AM2238
FastAP enzyme	ThermoFisher	Cat# EF0651
Dynabeads MyOne Silane	ThermoFisher	Cat# 37002D
T4 RNA ligase	NEB	Cat#M0204L
AffinityScript RT Enzyme	Agilent	Cat#600107
Phusion Master Mix	NEB	Cat# M0531L
AMPure XP Beads	Beckman Coulter	Cat# B23318
IDT indexes	IDT	N/A
ChIP-seq reagents
Protein G beads	ThermoFisher	Cat#10003D
RNAse	Roche	Cat#11119915001
Proteinase K	Invitrogen	Cat# 25530-015
DNA end-repair kit	Epicenter Biotech	Cat# ER0720
Klenow Fragment	NEB	Cat# M0212L
Quick Ligation kit	NEB	Cat# M2200S
PFU Ultra II HS 2x Master Mix	Agilent	Cat#600850-51
Amplicon-seq reagents and primers
QIAamp DNA Micro Kit	QIAGEN	Cat#6304
DNeasy Blood and Tissue Kit	QIAGEN	Cat#69504
Titanium® Taq DNA Polymerase	Takara	Cat# 639208
Agencourt AMPure XP SPRI beads	Beckman Coulter	Cat# A63880
P5 Primer for tiling: AATGATACGGCGAC CACCGAGATCTACACTCTTTCCCTACAC GACGCTCT TCCGATCT TTGTGGAAAGGACGAAACACCG	IDT	N/A
P7 Primer for tiling: CAAGCAGAAGACGG CATACGAGATNNNNNNNNGTGACTGGA GTTCAGAC GTGTGCTCTTCCGATCTCCAATTCCCAC TCCTTTCAAGACCT	IDT	N/A
sg#70 amplicon F-primer: GGTGAGACG TCAGAAAGGAAGT	IDT	N/A
sg#70 amplicon R-primer: AATTCACCC ACTGAAAGGAAAA	IDT	N/A
Software and algorithms
CRISPResso2	Clement et al.29	http://crispresso.pinellolab.org/submission/
EQTLGEN	Võsa et al.28	https://eqtlgen.org/cis-eqtls.html
Python v3.9		http://www.python.org/downloads/release/python-390/
R v4.2		http://www.r-project.org/
Bioconductor v3.15		http://www.bioconductor.org/
DESeq v2	Anders and Huber43	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
CSAW	Lun et al.44	https://bioconductor.org/packages/release/bioc/html/csaw.html
ComplexHeatmap	Gu et al.45	https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
Enformer v1	Avsec et al.5	https://tfhub.dev/deepmind/enformer/1
Enformer fine-tuning code for this paper		https://doi.org/10.5281/zenodo.7775557, https://github.com/BernsteinLab/BE_CD69_paper_2022
DeepTools 3.5.0	Ramirez et al.46	https://github.com/deeptools/deepTools
TFModisco 0.4.2.3	Shrikumar et al.47	https://github.com/kundajelab/tfmodisco
MEME suite v5.4.1	Bailey et al.48	https://meme-suite.org/meme/
ENCODE ATAC-seq pipeline v 2.1.3		https://github.com/ENCODE-DCC/atac-seq-pipeline
ENCODE ChIP-seq pipeline v 2.1.6		https://github.com/ENCODE-DCC/chip-seq-pipeline2
STAR v2.7.9a	Dobin et al.49	https://github.com/alexdobin/STAR
Salmon v1.6	Patro et. al50	https://github.com/COMBINE-lab/salmon
Bedtools v2.30.0	Quinlan et al.51	https://github.com/arq5x/bedtools2
Samtools v1.12	Li et al.52	https://github.com/samtools/samtools
MOODS v1.9.4.1	Korhonen et al.53	https://github.com/jhkorhonen/MOODS
Deposited data
Jurkat ATAC-seq, wild-type	Nasser et al.4	GEO: GSE155555
CD4+ T-cell ATAC-seq		GEO: GSE124867
Jurkat RNA-seq, wild-type	Brignall et al.54	GEO: GSE90718
+/- edited Jurkat ChIP-seq, ATAC-seq	this paper	GEO: GSE206377
+/- BHLHE40-OE Jurkat RNA-seq, ChIP-seq, ATAC-seq	this paper	GEO: GSE206377