Summary of RNA-Seq analysis of abdominal fat in divergent FL and LL chickens at 7 wk.

Read trimming, read mapping and expression data are provided for three different sequencing schemes utilized for paired-end sequencing of 8 libraries (4 FL and 4 LL cockerels). Values are averaged across 3–4 individual birds per genotype. In Scheme A, two sequencing lanes were used for assignment of two FL and two LL libraries per lane (n = 4/lane).
*Two libraries (1 FL and 1 LL) in sequencing lane 2 (Scheme A) had a low QC score; therefore, their low-quality data were eliminated from further RNA-Seq analysis under this scheme. Consequently, these two libraries were each re-sequenced in individual lanes in Scheme B (n = 1/lane). Finally, all eight libraries (4 FL and 4 LL) were sequenced in two replicate lanes in Scheme C (n = 8/lane). Scheme C provides the most robust RNA-Seq design, the balanced block design; where, all eight libraries (4 FL and 4 LL) are sequenced in two replicate sequencing lanes. This design allows the targeted biological variation to be partitioned from technical error as described in detail by Auer and Doerge [51]. Additional information on RNA-Seq analysis is provided in S2 Table.
Abbreviations: fat line (FL), lean line (LL), and million (M).
Summary of RNA-Seq analysis of abdominal fat in divergent FL and LL chickens at 7 wk.