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E-GEOD-76841 - Characterisation of the whole blood mRNA transcriptome in Holstein-Friesian and Jersey calves in response to gradual weaning

Status
Released on 19 August 2016, last updated on 12 September 2016
Organism
Bos taurus
Samples (48)
Protocols (3)
Description
The objectives of the study were to use RNA-Seq to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1) and 8 days after weaning (d 8). RNA-seq analysis was carried out on RNA extracted from whole blood. Gradual weaning had no effect on gene expression (P>0.05).There were 550 differentially expressed genes at a false discovery rate of 10% and with a ≥1.5-fold change, between Holstein-Friesian and Jersey calves on d -14, 490 on d 1, and 411 on d 8. GOseq/KEGG pathway analysis showed that the cytokine-cytokine receptor interaction pathway and the neuroactive ligand-receptor interaction pathway were over-represented between breeds on all days (P<0.01; Q≤0.1). These results demonstrate that the gradual weaning practiced here does not compromise the welfare of artificially-reared dairy calves, evidenced by the lack of expression changes in any genes in response to gradual weaning. These data also suggest differences in cell signalling and immune responses between breeds. Eight Holstein-Friesian and eight Jersey bull calves were group housed indoors and individually fed milk replacer and concentrate using an automatic feeder. Calves were gradually weaned by reducing milk-replacer from 6 litres to 0 litres over 14 days (d) (d -13 to d 0). Calves were blood sampled on d -14, 1, and 8, relative to weaning (d 0). RNA-seq analysis was carried out on RNA extracted from whole blood.
Experiment type
RNA-seq of coding RNA 
Contacts
Dayle Johnston <dayle.johnston@teagasc.ie>, Alan K Kelly, Bernadette Earley, David A Kenny, Mark McGee, Matthew S McCabe, Paul Cormican, Sinead M Waters
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-76841.idf.txt
Sample and data relationshipE-GEOD-76841.sdrf.txt
Additional data (1)E-GEOD-76841.additional.1.zip
Links