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

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

Udder quarter treatment Animal No. Sample treatmenta 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
  1. 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)