Table 2.

Example of a properly-formatted reads file for mock data of one gene pair. Lines 1 and 2 represent combinatorial-targeting guides knocking out both ARID1A and ARID1B simultaneously, lines 3–6 represent single-targeting guides knocking out either ARID1A (lines 3–4) or ARID1B (lines 5–6) paired with a negative control guide in both orientations, and lines 7–8 represent dual-targeting guides cutting either ARID1A (line 7) or ARID1B (line 8) twice. Guide sequences and read counts are mock data for illustrative purposes.

gene1	gene2	Cas9 guide	Cas12a guide	T0 reads	T18 reads
ARID1A	ARID1B	AATG	TTGC	45	0
ARID1B	ARID1A	CGAC	TATT	54	1
ARID1A	NegControl	AATG	CGCT	70	60
NegControl	ARID1A	GGTA	TATT	82	75
ARID1B	NegControl	CGAC	CGCT	61	87
NegControl	ARID1B	GGTA	TTGC	76	92
ARID1A	None	AATG	TATT	91	42
ARID1B	None	CGAC	TTGC	63	53