A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Halstead, Michelle M.; Kern, Colin; Saelao, Perot; Wang, Ying; Chanthavixay, Ganrea; Medrano, Juan F.; Van Eenennaam, Alison L.; Korf, Ian; Tuggle, Christopher K.; Ernst, Catherine W.; Zhou, Huaijun; Ross, Pablo J.

doi:10.1186/s12864-020-07078-9

BMC Genomics

Table 1 ATAC-seq data preprocessing. Per library, total raw reads, mapped reads (excluding mitochondrial DNA), duplicate reads, informative reads (monoclonal and uniquely mapping), and percent of raw reads that were informative

From: A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Species	Tissue	Replicate	Raw reads	Mapped reads	Duplicate reads	Informative reads	% Raw
Cattle	Adipose	A	152,184,070	145,648,161	82,972,324	37,815,392	24.85
	Adipose	B	126,920,776	123,879,749	25,466,938	72,623,985	57.22
	Cerebellum	B	158,964,554	134,391,900	53,303,886	49,305,250	31.02
	Brain Cortex	A	216,202,716	189,763,599	122,567,574	30,997,045	14.34
	Brain Cortex	B	205,363,760	174,961,995	96,411,128	41,021,487	19.98
	Hypothalamus	A	146,439,048	102,771,471	50,044,176	35,090,140	23.96
	Hypothalamus	B	68,153,356	63,771,723	31,495,325	15,328,535	22.49
	Liver	A	175,124,072	165,112,503	95,001,248	40,031,560	22.86
	Liver	B	194,367,992	179,265,341	99,942,567	36,472,289	18.76
	Lung	A	163,469,102	159,710,295	27,682,063	99,691,291	60.98
	Lung	B	190,030,170	184,571,092	36,657,121	110,584,502	58.19
	Muscle	A	89,174,618	86,045,857	15,262,767	55,794,693	62.57
	Muscle	B	97,247,280	69,592,640	10,539,048	45,909,945	47.21
	Spleen	A	261,785,316	250,911,567	163,860,741	37,521,241	14.33
	Spleen	B	179,854,284	162,449,025	51,533,284	69,626,100	38.71
Pig	Adipose	A	93,118,998	87,025,520	15,814,107	57,651,677	61.91
	Adipose	B	71,639,956	66,597,412	12,368,404	42,960,583	59.97
	Cerebellum	A	186,388,542	175,280,070	90,013,906	63,538,783	34.09
	Cerebellum	B	125,817,350	116,536,743	41,557,703	57,997,395	46.10
	Brain Cortex	A	101,924,240	98,384,411	36,110,627	53,096,952	52.09
	Brain Cortex	B	160,871,726	155,783,257	77,377,043	66,403,810	41.28
	Hypothalamus	A	112,463,726	106,966,835	52,803,730	39,919,895	35.50
	Hypothalamus	B	170,163,006	162,907,052	92,303,710	56,125,160	32.98
	Liver	A	171,864,386	167,321,556	113,588,699	42,376,220	24.66
	Liver	B	169,952,062	164,205,920	85,279,200	64,117,458	37.73
	Lung	A	108,086,464	104,424,556	19,658,156	73,018,749	67.56
	Lung	B	110,690,180	106,275,981	17,791,030	74,869,852	67.64
	Muscle	A	168,211,474	165,225,305	41,747,860	113,058,649	67.21
	Muscle	B	141,069,686	138,785,466	39,577,315	91,780,486	65.06
	Spleen	A	91,549,652	88,698,199	13,254,769	64,352,893	70.29
	Spleen	B	93,747,292	90,558,895	12,817,045	67,241,934	71.73

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ISSN: 1471-2164

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