REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
APC Rat anti-Mouse CD45	BD Pharmingen	clone 30-F11
FITC Rat anti-Mouse CD45	BD Pharmingen	clone 30-F11
FITC Mouse anti-Human CD45	BD Pharmingen	clone HI30
V450 Mouse anti-Human CD45	BD Pharmingen	clone HI30
BV421 Mouse anti-Human CD3	BD Pharmingen	clone SK7
BV421 Mouse anti-Human CD56	BD Pharmingen	clone NCAM16.2
V450 Mouse anti-Human CD19	BD Pharmingen	clone SJ25C1
FITC Mouse anti-Human CD33	BD Pharmingen	clone HIM3-4
BV421 Mouse anti-Human CD34	BD Pharmingen	clone 581
MACS microbeads, anti-human CD34	Milltenyi	Cat# 130-046-702
MACS microbeads, anti-human glycophorin A	Milltenyi	Cat# 130-050-501
Biological samples
CD34+ cells from 1 individual with sickle cell disease	Clinical trial discard material obtained with informed consent, CD34+ cells isolated by Allcells, Inc.	N/A
Chemicals, peptides, and recombinant proteins
S.pyogenes Cas9 protein, wild-type	Berkeley MacroLab	N/A
S.pyogenes Cas9 protein, HF-1 mutant	Berkeley MacroLab	N/A
S.pyogenes Cas9 protein, espCas9-1.1 mutant	Berkeley MacroLab	N/A
S.pyogenes Cas9 protein, AltR-HiFi mutant	IDT, Inc. or Aldevron Inc. (as SpyFI Cas9)	IDT cat #10007803; Aldevron cat #MRD032-3
Deposited data
Sequencing data including DNA genotyping and RNA-seq	NCBI SRA archive	Accession ID: PRJNA498110
Experimental models: Organisms/strains
Mouse, age 7-8 weeks, strain NBSGW: NOD.Cg-KitW−41JTyr + PrkdcscidIl2rgtm1Wjl/ThomJ	Jackson Labs	Strain ID: 026622
Oligonucleotides
ssDNA CJ6A	IDT, Inc. [Ultramer], and Trilink Inc.	Unmodified ssDNA with sequence 5′-TCAGGGCAGAGCCATCTATTGC TTACATTTGCTTCTGACACAACTGT GTTCACTAGCAACCTCAAACAGAC ACCATGGTGCACCTGACTCCTG TGGAGAAGTCTGCCGTTACTGCC CTGTGGGGCAAGGTGAACGTGG ATGAAGTTGGTGGTGAGGCCCTG GGCAGGT-3′
NGS primer: OT1 F Stubbed	IDT, Inc.	GCTCTTCCGATCTtaccctttcccgttctccac
NGS primer: OT1 R Stubbed	IDT, Inc.	GCTCTTCCGATCTggtacggcctaaga aattatagtttagc
NSG primer: OT2 F stubbed	IDT, Inc.	GCTCTTCCGATCTtagacctgcctccttcagg
NSG primer: OT2 R stubbed	IDT, Inc.	GCTCTTCCGATCTcttcgcttccatctgatcagg
NGS primer: HBB F stubbed	IDT, Inc.	GCTCTTCCGATCTTAGGGTTGGCCAAT CTACTCC
NGS primer: HBB R stubbed	IDT, Inc.	GCTCTTCCGATCTTGGGAAAATAGACC AATAGGCAGAG
Pooled-primer reagent for all other off-targets	See Table S5	See Table S5
sgRNA 3xMS-G10	Synthego, Inc.	20 nt Protospacer: 5′-CUUGCCCCACAGG GCAGUAA-3′
Software and algorithms
Seurat	https://satijalab.org/seurat/index.html	N/A
Bowtie2	http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml	N/A
kallisto 0.43.1	https://pachterlab.github.io/kallisto/about	N/A
cortado	https://zenodo.org/record/6394892	https://doi.org/10.5281/zenodo.6394892
FreeBayes	Erik Garrison, Gabor Marth	https://doi.org/10.48550/arXiv.1207.3907
GUIDE-seq	https://github.com/tsailabSJ/guideseq	N/A