Chicken spleens, bursas and BMDMs +/- LPS (all from F2 generation: offspring of the brother-sister mating of F1 progeny from a defined parental cross)

This dataset comprises RNA sequencing of chicken (Gallus gallus) spleens, bursa and bone marrow derived macrophages (BMDMs), both unstimulated and 24 hours after stimulation with lipopolysaccharide (LPS). These birds were the progeny of sibling matings - after mating selected broiler-layer pairs (Ross 308 and CSF1R-MacApple transgenic ISA Brown, respectively), cohorts of F2 birds were generated from sibling matings of the F1 generation.To identify functional allelic variants using RNA-seq requires the presence of informative expressed SNVs in each individual. The approach used here is one specifically applicable to birds because they are multiparous - if brother-sister mating F1 progeny from a defined parental cross, this would generate an F2 population in which the grandparental allelic variants at each locus will be homozygous in a subset of birds. This dataset, therefore, exposes high and low expression alleles that are masked in heterozygotes.All libraries were 75 base pairs paired-end mRNA-seq, generated by Edinburgh Genomics and sequenced at a depth of >40 million reads using an Illumina HiSeq 4000, following the Illumina TruSeq mRNA (polyA-selected) library preparation protocol.