Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens

Table 1 Genomic alignments for guides targeting SOX9 and SOX10 in the Avana library

	Type	On-target	Off-target	Spacer sequence	BaseSub	Chr	Pos
Guide A1	PM	SOX9		GCTCGGACACCGAGAACACG		17	72,121,509
Guide A2	PM	SOX9		GCAGCACAAGAAGGACCACC		17	72,122,775
	MM		SOX10	GCAGCACAAGAA-GACCACC	G →A	22	37,978,058
Guide A3	PM	SOX9		GCACCTGGCTGACCGCCTCG		17	72,121,612
	MM		SOX10	GCACCTGGCTGAC-GCCTCG	C →G	22	37,983,546
Guide A4	PM	SOX9		GCTGGTACTTGTAATCCGGG		17	72,122,793
	MM		SOX10	GCTGGTACTTGTA-TCCGGG	A →G	22	37,978,040
Guide B1	PM	SOX10		ACAAGTACCAGCCCAGGCGG		22	37,978,032
Guide B2	PM	SOX10		GTAGTGGGCCTGGATGGCGG		22	37,977,942
Guide B3	PM	SOX10		GCACCTGGCTGACGGCCTCG		22	37,983,546
	MM		SOX9	GCACCTGGCTGAC-GCCTCG	G →C	17	72,121,612
Guide B4	PM	SOX10		GCTGGTACTTGTAGTCCGGG		22	37,978,040
	MM		SOX9	GCTGGTACTTGTA-TCCGGG	G →A	17	72,122,793
	MM		SOX8	GCTGGTACTTGTAGTC-GGG	C →G	16	983,802

PM perfect match alignment, MM single-mismatch alignment, BaseSub base substitution in the protospacer sequence

ISSN: 1474-760X