Online-Only Table 2.

Whole Genome Sequencing (WGS) data sets for Formalin-Fixed Paraffin-Embedded (FFPE) process with fixation time of 1, 2, 6, or 24 hours for DNA extracted from HCC1395BL and HCC1395 cell lines.

Sample ID	Sample	Biosample	Platform	Machine model	library Protocol (Input amount	Total Reads	Total Reads After Trimming	Percent Total Reads after Trimming	Total Mapped Reads	Percent Total Mapped Reads (Trimmed)	Percent Non-duplicated Reads (Mapped Trimmed)	Mean Coverage Depth	Mean Coverage Depth SD	Percent of Coverage >  = 5X	Percent of Coverage >  = 15X	Percent of Coverage >  = 30X	Percent GC	Median Insert Size
FFG_IL_N_1h	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,765,128,404	1,764,489,856	99.96	1,755,040,098	99.46	81.33	60.73	275.63	93.45	92.21	86.08	42.39	263
FFG_IL_N_24h	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,639,966,382	1,639,566,366	99.98	1,630,268,029	99.43	83.76	58.14	273.91	93.45	92.28	85.66	40.35	258
FFG_IL_N_2h	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,068,216,980	2,067,386,842	99.96	2,058,632,971	99.58	76.51	73.91	352.49	93.54	92.83	89.46	42.15	251
FFG_IL_N_6h	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,524,211,818	1,523,752,982	99.97	1,516,101,932	99.50	81.66	53.68	279.78	93.44	91.89	83.37	41.94	264
FFG_IL_T_1h	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,624,805,980	2,622,947,802	99.93	2,604,551,075	99.30	76.27	89.63	321.88	92.93	92.30	89.27	39.73	277
FFG_IL_T_24h	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,721,612,052	1,721,231,716	99.98	1,710,443,429	99.37	84.68	59.41	477.62	92.99	91.52	81.57	39.43	269
FFG_IL_T_2h	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,962,242,886	1,961,844,318	99.98	1,953,044,006	99.55	82.43	69.99	319.98	92.88	91.50	84.05	39.61	265
FFG_IL_T_6h	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,943,133,326	2,941,257,406	99.94	2,918,794,880	99.24	75.07	100.42	608.82	93.06	92.71	90.90	40.19	306
FFG_GZ_N_1h-B	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,149,948,070	2,149,439,522	99.98	2,136,427,075	99.40	86.88	67.84	319.70	93.54	92.37	85.63	40.12	247
FFG_GZ_N_1h-F	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,403,027,922	2,401,640,844	99.94	2,392,089,625	99.60	85.68	77.14	194.74	93.38	92.37	89.44	41.62	238
FFG_GZ_N_24h-B	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,460,398,476	2,459,792,090	99.98	2,448,071,395	99.52	85.20	78.05	649.98	93.68	93.33	91.38	41.19	244
FFG_GZ_N_24h-C	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,761,455,916	1,756,523,044	99.72	1,746,804,745	99.45	84.75	54.76	190.92	93.28	91.67	84.17	41.39	232
FFG_GZ_N_24h-F	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,113,753,208	2,112,823,428	99.96	2,104,899,010	99.63	87.70	68.93	250.14	93.44	92.41	87.92	40.72	227
FFG_GZ_N_2h-A	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	3,121,263,208	3,109,608,214	99.63	3,095,791,797	99.56	75.15	97.51	620.28	93.71	93.34	91.95	41.61	242
FFG_GZ_N_2h-E	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,844,864,910	1,842,574,250	99.88	1,835,180,122	99.60	87.31	58.71	163.92	93.29	91.83	85.43	40.76	253
FFG_GZ_N_6h-A	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,348,616,522	2,347,656,712	99.96	2,336,897,178	99.54	85.56	74.84	552.08	93.66	93.27	90.84	41.44	249
FFG_GZ_N_6h-E	HCC1395BL	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,324,253,696	2,322,277,434	99.92	2,312,897,831	99.60	85.59	74.02	270.78	93.48	92.60	89.34	41.11	248
FFG_GZ_T_1h-A	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,173,073,798	2,172,389,654	99.97	2,161,992,309	99.52	85.94	66.90	653.36	93.01	91.95	84.29	41.64	256
FFG_GZ_T_1h-B	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,631,699,638	1,618,249,558	99.18	1,610,013,338	99.49	82.37	51.10	105.70	92.36	89.26	75.89	40.67	253
FFG_GZ_T_1h-E	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,441,354,752	2,440,848,016	99.98	2,431,265,220	99.61	86.43	78.56	156.28	92.75	91.44	86.19	40.18	252
FFG_GZ_T_24h-B	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,517,517,314	2,516,534,444	99.96	2,506,328,630	99.59	84.68	80.08	489.37	93.04	92.53	88.90	41.49	249
FFG_GZ_T_24h-F	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	3,096,658,362	3,095,956,264	99.98	3,082,562,699	99.57	84.29	98.75	295.06	92.97	92.31	89.34	39.91	257
FFG_GZ_T_2h-A	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,281,259,460	2,279,880,072	99.94	2,265,837,473	99.38	82.69	71.81	577.42	93.02	92.19	86.23	41.71	243
FFG_GZ_T_2h-B	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	1,844,049,210	1,833,063,922	99.40	1,823,246,662	99.46	80.78	59.04	146.98	92.69	90.75	81.60	41.32	242
FFG_GZ_T_6h-A	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,133,526,796	2,132,509,862	99.95	2,123,023,988	99.56	82.75	66.89	556.68	93.01	92.08	85.27	41.58	246
FFG_GZ_T_6h-B	HCC1395	FFPE	HiSeq	HiSeq 4000	NEBNext Ultra II (200 ng)	2,891,641,362	2,879,535,806	99.58	2,863,935,742	99.46	75.53	92.64	245.11	92.93	92.21	89.40	40.97	236

Libraries were made from NEBNext Ultra II (200 ng) library protocol and sequenced on Illumina HiSeq 4000.