REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
NEB 5-alpha	New England Biolabs	C2987
pcDNA3-mRuby2	Addgene	40260
pEF-GFP	Addgene	11154
pENTR CMV-mRuby-bGH	Twist Biosciences	N/A
Chemicals, peptides, and recombinant proteins
Q5 High-Fidelity 2X Master Mix	New England Biolabs	M0492S
Gibson Assembly Master Mix	New England Biolabs	E2611L
Human IL-2	Peprotech	200-02
Alt-R crRNA	IDT	N/A
Alt-R tracrRNA	IDT	1072534
Alt-R SpCas9 Nuclease V3	IDT	1081059
CRISPRevolution sgRNA EZ Kit	Synthego	N/A
SpCas9 2NLS Nuclease	Synthego	N/A
Critical commercial assays
SPRIselect	Beckman Coulter	B23318
SF Cell line kit	Lonza	V4XC-2012
SE Cell line kit	Lonza	V4XC-1012
P3 Primary Cell kit	Lonza	V4XP-3032
Dynabeads Human T-Activator CD3/CD28	Thermo Fischer Scientific	11161D
EasySep Human T Cell Isolation kit	Stemcell Technologies	17951
Lipofectamine CRISPRMAX Cas9 Transfection Reagent	Thermo Fischer Scientific	CMAX00001
PureLink Genomic DNA extraction kit	Thermo Fischer Scientific	K1820-01
Zymoclean Gel DNA Recovery Kit	Zymo Research	D4001
TOPO-vector using Zero-blunt TOPO PCR Cloning Kit	Thermo Fischer Scientific	450245
PureLink RNA Mini Kit	Thermo Fischer Scientific	12183018A
RiboCop rRNA Depletion Kit	Lexogen	144
SuperScript Double-Stranded cDNA Synthesis Kit	Thermo Fischer Scientific	11917010
ZR Plasmid Miniprep - Classic kit	Zymo Research	D4015
Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3	10-X Genomics	PN-1000075
Chromium Single Cell B Chip	10-X Genomics	1000074
Deposited data
Predicted GSH sites	This paper-Table S1	N/A
Bulk RNA-sequencing data	This paper	ENA: E-MTAB-11289
Single-cell RNA-sequencing data	This paper	ENA: E-MTAB-11289
Protein coding gene coordinates	GENCODE gene annotation (Release 24)	https://www.gencodegenes.org/human/release_24.html
Oncogenes coordinates	Cancer Gene Census	https://cancer.sanger.ac.uk/census
miRNA coordinates	MirGeneDB	Fromm et al. (2020)
Enhancer coordinates	EnhancerAtlas 2.0	Gao and Qian (2019)
tRNA coordinates	GENCODE gene annotation (Release 24)	https://www.gencodegenes.org/human/release_24.html
lncRNA coordinates	GENCODE gene annotation (Release 24)	https://www.gencodegenes.org/human/release_24.html
Telomere coordinates	UCSC genome browser GRCh38/hg38	https://genome.ucsc.edu
Centromere coordinates	UCSC genome browser GRCh38/hg38	https://genome.ucsc.edu
Experimental models: Cell lines
HEK293T cell line	ATCC	CRL-3216
Jurkat E6-1 T cell line	ATCC	TIB152
Human PBMC	Stemcell Technologies	70025
Neonatal human dermal fibroblasts	Coriell Institute	GM03377
Oligonucleotides
Rogi1/2 genotyping primers	This paper-Table S3	N/A
Recombinant DNA
LAMB3 cDNA	Genscript	NM_000228.3
Rogi1 HDR mRuby donor	This paper	Addgene #179860
Rogi2 HDR mRuby donor	This paper	Addgene #179861
Rogi1 HDR LAMB3-T2A-GFP donor	This paper	Addgene #179864
Rogi2 HDR LAMB3-T2A-GFP donor	This paper	Addgene #179865
AAVS1/CCR5 MMEJ PITCh mRuby donors	This paper	N/A
GSH1, 2, 7, 8, 31 MMEJ PITCh mRuby donors	This paper	N/A
Software and algorithms
GSH prediction algorithm	This paper	https://doi.org/10.5281/zenodo.5786825
BEDtools	Quinlan and Hall (2010)	http://github.org/pezmaster31/bamtools
Platypus	Yermanos et al. (2021)	https://github.com/alexyermanos/Platypus
GraphPad Prism v8.3.1 for MacOS	GraphPad software	N/A
Subread v1.6.2	Liao et al. (2013)	http://subread.sourceforge.net
Rsubread	Liao et al. (2014)	https://bioconductor.org/packages/release/bioc/html/Rsubread.html
edgeR	Robinson et al. (2010)	https://bioconductor.org/packages/release/bioc/html/edgeR.html
CellRanger	10XGenomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Seurat	Stuart et al. (2019)	https://satijalab.org/seurat/
Harmony	Korsunsky et al. (2019)	https://portals.broadinstitute.org/harmony/
Genenious Prime 2019.2.3	Biomatters Ltd.	N/A
FlowJo 10.8	Becton Dickinson & Company	N/A