Table 1 De novo TE insertions detected and PCR validated in miPSC lines

From: Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells

Insertion #	Subfamily	Location	Monomers	EN motif	TSD (bp)	PolyA (bp)	Origin	Detected by
miPSC_1_L1	T_F	1q	6.8	TCTT/AG	16	~125	Reprogramming	WGS + mRC-seq
miPSC_2_L1	T_F	10q	0	TTCT/GT	14	>100	Mosaic	WGS + mRC-seq
miPSC_3_L1	T_F	13q	5.8	ATTC/AA	15	~50	Reprogramming	WGS + mRC-seq
miPSC_4_L1	T_F	3q	5.3	TCTT/AA	13	~54	Reprogramming	WGS + mRC-seq
miPSC_5_L1	G_F	19q	2	TTAT/AT	14	~50	Reprogramming	WGS + mRC-seq
miPSC_6_L1	T_F	7q	0	TTTA/AA	17	~51	Reprogramming	WGS + mRC-seq
miPSC_7_L1	G_F	Xq	5	TCTT/AT	16	>80	Reprogramming	WGS + mRC-seq
miPSC_8_L1	T_F	19q	3.7	TTTC/AA	19	~24	Reprogramming	WGS + mRC-seq
miPSC_9_B2	B2	11q	NA	TCTT/AC	16	>60	Reprogramming	WGS + mRC-seq
miPSC_10_L1	T_F	12q	0	TTTT/GT	6	~36*	Reprogramming	WGS
miPSC_11_B2	B2	13q	NA	TTTT/GA	14	>73	Reprogramming	WGS + mRC-seq
miPSC_12_L1	T_F	13q	0	TCTT/AG	17	~97	Reprogramming	WGS + mRC-seq
miPSC_13_L1	A	14q	3	TTTC/AT	13	~46	Reprogramming	WGS + mRC-seq
miPSC_14_B2	B2	15q	NA	TTTT/AC	16	>66	Reprogramming	WGS + mRC-seq
miPSC_15_L1	G_F	2q	0	TTTC/AA	17	~28*	Reprogramming	WGS
miPSC_16_L1	T_F	2q	>3	TTTT/AA	16	>100	Reprogramming	WGS + mRC-seq
miPSC_17_L1	T_F	3q	>3	ACTT/AA	14	~45	Reprogramming	WGS + mRC-seq
miPSC_18_B1	B1	3q	NA	TTTT/AA	15	~30	Reprogramming	WGS + mRC-seq
miPSC_19_L1	T_F	3q	>3	GTTT/AT	15	>80	Reprogramming	WGS + mRC-seq
miPSC_21_L1	T_F	4q	0	TTTT/CA	17	>150	Reprogramming	WGS + mRC-seq
miPSC_22_B2	B2	6q	NA	TCTT/GA	15	~52	Reprogramming	WGS + mRC-seq
miPSC_23_B2	B2	9q	NA	TTTT/AT	16	~50	Mosaic	WGS + mRC-seq
miPSC_24_B2	B2	Xq	NA	TTTT/AA	15	>100	Reprogramming	WGS + mRC-seq
miPSC_26_L1	T_F	1q	>3	TCTT/AT	22	~58	Reprogramming	WGS + mRC-seq
miPSC_27_B2	B2	11q	NA	TTTC/AA	14	>60	Reprogramming	WGS + mRC-seq
miPSC_28_L1	T_F	13q	3.6	TCCT/AA	15	~93*	Reprogramming	mRC-seq
miPSC_29_L1	T_F	15q	0	TCTT/AA	16	>80	Reprogramming	WGS + mRC-seq
miPSC_30_L1	T_F	6q	>3	TCTT/AT	16	~72	Reprogramming	mRC-seq
miPSC_31_L1	T_F	7q	>3	TTTG/AC	15	~43	Reprogramming	mRC-seq
miPSC_32_L1	T_F	Xq	2	TCTT/AT	13	~37	Reprogramming	WGS + mRC-seq
miPSC_33_L1	G_F	Xq	>3	TTTT/AA	15	~47	Reprogramming	mRC-seq
miPSC_34_L1	T_F	8q	0	TCTT/AA	6	~36*	Reprogramming	WGS + mRC-seq
miPSC_35_L1	T_F	1q	0	TTTA/AA	15	~38	Reprogramming	WGS + mRC-seq
miPSC_36_L1	G_F	8q	0	ATGT/GA	6	~42	Reprogramming	WGS + mRC-seq
miPSC_37_L1	T_F	1q	1.2	TTTT/GT	14	~20	Reprogramming	WGS + mRC-seq
miPSC_38_L1	T_F	10q	0	TTCT/AA	15	~55	Reprogramming	WGS + mRC-seq
miPSC_39_L1	T_F	10q	0	TTTT/AA	8	>140*	Reprogramming	WGS + mRC-seq
miPSC_40_L1	T_F	11q	>3	TTTT/GA	14	>120	Reprogramming	WGS + mRC-seq
miPSC_41_L1	T_F	12q	2.6	TCTT/GC	16	~49	Reprogramming	mRC-seq
miPSC_42_B1	B1	14q	NA	TTCT/AA	15	>50	Reprogramming	mRC-seq
miPSC_43_L1	T_F	16q	>3	ATTT/AA	14	~42*	Mosaic	WGS + mRC-seq
miPSC_69_L1	T_F	13q	2	CTTT/AT	16	~61	Mosaic	WGS (ONT)
miPSC_87_L1	T_F	17q	0	TTTT/GT	16	~21	Reprogramming	WGS (ONT)

Insertions marked with an asterisk carry a 3′ transduction. miPSC_1_L1 - miPSC_8_L1 were detected in adult primary cell-derived bulk miPSCs, miPSC_9_B2 - miPSC_43_L1 in MEF-derived single-cell miPSC clones, and miPSC_69_L1 and miPSC_87_L1 in MEF-derived bulk miPSCs. Unless stated otherwise, insertions were detected by Illumina sequencing.

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Table 1 De novo TE insertions detected and PCR validated in miPSC lines

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