Development and evaluation of a milk protein transcript depletion method for differential transcriptome analysis in mammary gland tissue

Table 1 Read statistic of raw data, after quality trimming and read alignment to the bovine genome

Udder quarter treatment	Animal No.	Sample treatment^a	RIN value	Reads (total number)	Reads after quality trimming (%)	Mapped reads (%)
Non-challenged	Cow1	0	7.7	77,920,096	90	98
		A	4.9	70,975,008	77	97
		B	4.6	81,396,012	91	98
	Cow2	0	7.8	78,859,264	90	98
		A	4.9	80,349,800	90	98
		B	5.4	78,824,666	89	98
	Cow3	0	8.1	80,203,836	90	99
		A	5.1	62,510,886	89	98
		B	5.6	74,101,514	89	98
Challenged	Cow1	0	7.9	78,564,210	90	98
		A	4.7	78,719,102	90	98
		B	4.9	80,990,200	89	98
	Cow2	0	9.6	92,966,426	89	98
		A	5.9	63,610,608	88	95
		B	6.9	70,529,798	89	97
	Cow3	0	7.8	85,090282	89	98
		A	6.0	81,278,402	89	98
		B	5.7	88,169,812	89	98

^aPathogen challenged and non-challenged udder tissue samples of the cows 1–3, each of them without RNA depletion (0) and with RNA depletion variant A (A) or variant B (B). Variant A and B differ in antisense oligonucleotide input for depletion (see Materials and Methods)

ISSN: 1471-2164