REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Human Peripheral Blood Leukopaks	STEMCELL Technologies	70500
Chemicals, peptides, and recombinant proteins
Cas9 protein (MacroLab, Berkeley	–	–
Lonza P3 buffer	Lonza, catalog no.	V4XP-3032
EasySep™ Human CD4+CD127lowCD25+ Regulatory T cell Isolation Kit	STEMCELL Technologies	18063
ImmunoCult™ Human CD3/CD28/CD2 T cell Activator	STEMCELL Technologies	10990
Critical commercial assays
RNA lysis buffer (Zymo, #R1060-1-100).	Zymo	R1060-1-100
Zymo-Quick RNA micro prep kit (#R1051)	Zymo	R1051
Turbo-DNAse (Fisher Scientific, AM2238)	Zymo	AM2238
RNA Clean & Concentrator-5 kit (Zymo, #R1016)	Zymo	R1016
QuantSeq FWD kit (Lexogen)	Lexogen	K0152x96-2-0162
Deposited data
RNAseq data for IEI and background TFs	GEO	GSE271788
RNAseq data from Freimer et al.14	GEO	GSE171737
Oligonucleotides
Custom crRNAs (Dharmacon) for CRISPR KO	–	See Table S9
Primers for genotyping	–	See Table S10
Dharmacon Edit-R CRISPR-Cas9 Synthetic tracrRNA	Dharmacon	U-002005-20
Single-stranded donor oligonucleotides (ssODN): TTAGCTCTGTTTACG TCCCAGCGGGCATGAGAGTAACA AGAGGGTGTGGTAATATTAC GGTACCGAGCACTATCGATACAAT ATGTGTCATACGGACACG	IDT custom oligo	N/A
Software and algorithms
Figure generation	Github	https://github.com/weinstockj/RNAseq-perturbation-CD4-pipeline
LLCB code	Github	https://github.com/weinstockj/LLCB
Other
96-well electroporation cuvette plate	Lonza	VVPA-1002