Milk somatic cells and fat globules transcriptome of an experimental challenge in 2 divergent lines for milk somatic cell count (SCC) of Alpine goats

Staphylococcus aureus is the major cause of very severe mastitis of dairy goats. We have designed an experimental model of infection of the goat mammary gland with S. aureus on two lines of goats (low, CCS-, and high, CCS+, somatic cell score lines).We have performed 2 challenges. The first one was described in Rainard et al. Vet Res (2018) 49:72, https://doi.org/10.1186/s13567-018-0564-4The second one, on the same goat lines, was performed in the same way, except that part of the animals were vaccinated. Phenotypic data for clinical score, cfu, antibody concentration together with metabolomic data on milk and blood were collected. We isolated 2 cell types: somatic cells and fat globules (should behave as epithelial mammary cells) from milk.24 goats were involved: 12 from CCS+ line and 12 from CCS- line, 12 were vaccinated and 12 were not. The time points were: 0, 12, 18, 24, 36, 44, 60 hours post-infection for milk and fat globules samples.RNASeq was performed at 0, 12, 18 h pi for fat globules and 18 and 44 h pi for somatic cells on20 animals. Some samples failed, so, we release here 77 samples with RNASeq data.Before sequencing, RNA was quantified by measuring the absorbance at 260 nm using a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA) and integrity was checked by Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA). cDNA libraries were prepared from the best quality RNA using an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturers instruction. Samples were amplified by PCR and quantified by qPCR. Individual RNA-seq libraries were sequenced using an Illumina HiSeq3000 sequencer (Illumina, San Diego, CA, USA) at the GenoToul genomic platform (Castanet-Tolosan, France).