Extended Data Table 2. BaseScope 1 probe controls in this study.

jglSH positive and negative control and experiments list. Exp=Experimental, Neg=negative control, Pos=positive control.

Junction	Target	Sample	Type	Probes	Figure Panel
Ex 16/17	DNA	Human nuclei +RNase	Exp	Sense	2c, 4b
			Exp	Anti-sense	2c
		Human nuclei +RNase +/− restriction enzyme (MluCI)	Neg	Sense	2e
				Sense	2e
		WT mouse nuclei +RNase	Neg	Sense	5g, d
		Mouse nuclei +RNase + Ex 16/17 DNA concatamer	Pos	Sense	5g
	RNA	Human tissue	Neg	Sense	EDT 4a
			Pos	Anti-sense	EDT 4a
IEJ 3/16	DNA	Human nuclei +RNase	Exp	Sense	2d, 4c
			Exp	Anti-sense	2d
		Human nuclei +RNase +/− restriction enzyme (PSTI & MslI)	Neg	Sense	2f
				Sense	2f
		WT Mouse nuclei +RNase	Neg	Sense	EDT 4b
	RNA	Human tissue	Neg	Sense	EDT 4b
			Pos	Anti-sense	5a