Table 1 Statistics analysis of clean reads mapping onto reference genome.

From: Multi-omics dataset of bovine mammary epithelial cells stimulated by ten different essential amino acids

Sample	Raw reads	Clean reads	Mapping efficiency	Phred> 20 (%)	Sample	Raw reads	Clean reads	Mapping efficiency	Phred >20 (%)
NEG_1	48,526,890	47,549,694	92.61%	96.85	Met_1	46,384,336	45,506,434	93.78%	96.19
NEG_2	43,176,084	42,530,258	92.74%	96.88	Met_2	41,498,318	40,413,838	93.45%	97.31
NEG_3	45,940,308	44,989,364	92.71%	96.73	Met_3	40,793,346	40,266,998	93.33%	97.35
NEG_4	45,406,952	44,616,416	92.71%	96.66	Met_4	43,268,450	427,36,254	93.03%	97.33
NEG_5	50,541,714	49,594,468	92.88%	96.79	Met_5	47,697,704	47,125,238	93.38%	97.35
NEG_6	46,829,238	46,111,516	92.94%	97.00	Met_6	45,551,840	44,703,604	93.52%	96.90
Arg_1	46,390,570	45,987,698	92.96%	97.35	Phe_1	47,526,272	46,582,198	93.02%	96.84
Arg_2	46,964,992	46,211,062	92.11%	97.22	Phe_2	47,428,866	46,399,916	93.30%	96.81
Arg_3	46,015,946	45,668,658	93.15%	96.84	Phe_3	53,705,974	52,418,068	92.90%	96.87
Arg_4	44,911,936	44,367,842	83.80%	97.30	Phe_4	46,669,402	45,601,374	92.69%	96.50
Arg_5	44,816,418	44,285,818	93.62%	97.21	Phe_5	50,288,164	49,017,216	92.47%	96.61
Arg_6	46,753,196	46,193,354	93.47%	97.12	Phe_6	51,493,910	49,931,934	92.55%	96.77
His_1	47,151,788	46,601,100	92.49%	97.10	Thr_1	46,907,428	45,578,642	93.25%	96.67
His_2	45,263,000	44,714,050	92.90%	96.90	Thr_2	53,469,642	52,135,856	93.44%	96.78
His_3	40,612,706	40,253,216	92.46%	97.10	Thr_3	45,859,072	44,557,912	92.85%	96.94
His_4	41,962,688	41,542,730	92.18%	97.25	Thr_4	50,051,988	48,869,674	93.29%	96.82
His_5	47,219,594	46,860,716	92.97%	97.41	Thr_5	47,181,948	46,294,180	93.25%	96.79
His_6	44,961,658	44,630,518	92.75%	97.09	Thr_6	45,299,044	44,021,930	92.32%	96.67
Ile_1	44,409,430	44,143,866	92.82%	97.28	Trp_1	45,961,922	44,819,548	93.18%	96.79
Ile_2	42,285,282	42,018,938	92.79%	96.82	Trp_2	45,661,406	43,839,576	92.11%	97.01
Ile_3	45,644,514	45,232,916	93.15%	96.90	Trp_3	45,596,684	44,770,264	93.58%	97.03
Ile_4	47,122,466	46,714,988	92.97%	96.97	Trp_4	46,588,266	45,742,108	92.20%	97.23
Ile_5	43,589,468	43,218,066	93.24%	97.23	Trp_5	45,209,728	43,980,576	92.38%	97.07
Ile_6	44,043,016	43,591,956	92.39%	96.9	Trp_6	45,515,404	44,238,466	91.39%	97.24
Leu_1	45,489,370	45,012,398	83.91%	97.22	Val_1	46,208,488	44,557,688	92.17%	97.32
Leu_2	46,056,674	45,504,358	93.09%	97.17	Val_2	45,995,318	44,540,748	91.72%	97.19
Leu_3	44,373,600	44,016,548	92.87%	97.28	Val_3	52,639,776	51,529,692	93.29%	95.92
Leu_4	44,005,676	43,663,748	92.79%	97.22	Val_4	44,879,374	43,045,218	93.40%	97.47
Leu_5	42,430,082	42,029,276	92.66%	97.33	Val_5	45,300,600	44,302,592	92.99%	97.10
Leu_6	44,428,110	43,925,098	93.46%	97.47	Val_6	47,799,064	46,034,646	93.95%	97.40
Lys_1	44,060,770	43,658,652	93.07%	97.18	POS_1	47,010,526	46,347,678	93.84%	97.71
Lys_2	45,720,748	45,363,288	93.50%	96.93	POS_2	43,969,636	42,918,656	92.93%	96.97
Lys_3	42,002,798	41,668,272	93.41%	96.57	POS_3	47,616,334	46,756,190	92.58%	97.15
Lys_4	41,221,456	40,887,146	93.18%	96.61	POS_4	47,351,276	45,510,318	91.82%	97.39
Lys_5	47,273,766	46,400,114	93.43%	97.04	POS_5	46,272,932	45,139,976	91.67%	97.25
Lys_6	46,279,044	45,825,968	93.05%	96.95	POS_6	47,241,486	46,172,198	91.83%	97.15

Complete DMEM-F12 medium used for BMECs was the positive control (POS) treatment, while DMEM-F12 medium without total essential amino acid served as the negative control (NEG) treatment. Ten treatments were NEG individually supplemented with L-arginine, L-histidine, L-isoleucine, L-leucine, L-lysine, L-methionine, L-phenylalanine, L-threonine, L-tryptophan or L-valine, respectively (n = 6). Individual EAA was supplemented to achieve a concentration equal to that in POS. After 6-h treatment, total RNA was extracted for latter RNA-seq.

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Table 1 Statistics analysis of clean reads mapping onto reference genome.

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