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Table 2 Percentage of fragments mapped to individual milk protein transcripts in relation to the total number of fragments in each sample as counted by featureCounts [50]

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 LALBA CSN1S1 CSN3 CSN2 CSN1S2 PAEP
Non-challenged Cow1 0 2.7 15.7 11.5 31.1 4.2 5.5
A 3.1 17.9 0.6 9.6 0.3 4.5
B 2.6 12.2 0.2 8.7 0.2 5.9
Cow2 0 0.8 18.7 9.6 14.3 4.9 3.9
A 0.5 18.7 0.8 3.1 0.1 2.2
B 0.4 16.4 0.2 2.8 0.1 2.0
Cow3 0 1.0 16.7 9.5 21.6 4.9 7.4
A 1.0 14.3 0.7 4.2 0.1 5.2
B 0.8 11.6 0.1 3.8 0.1 5.0
Challenged Cow1 0 1.1 15.2 11.1 21.9 3.3 4.3
A 1.0 12.1 0.6 5.9 0.1 3.8
B 0.9 9.0 0.2 5.4 0.0 4.0
Cow2 0 0.4 12.3 7.5 6.3 2.1 4.2
A 0.2 6.2 0.2 2.2 0.0 1.8
B 0.2 4.5 0.0 1.4 0.0 1.7
Cow3 0 0.0 0.1 0.5 0.1 0.0 0.0
A 0.0 0.1 0.0 0.0 0.0 0.0
B 0.0 0.0 0.1 0.0 0.0 0.0
  1. aUdder tissue samples without RNA depletion (0), with RNA depletion by variant A (A) or variant B (B). Variant A and B differ in antisense oligonucleotide input for depletion (see Materials and Methods)