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Gut microbiota of calves (whole meta-genome shotgun sequencing)

ABSTRACT: Gut microbiota of calves (whole meta-genome shotgun sequencing), treated or untreated with florfenicol.

PROVIDER: PRJEB33145 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3930920.fastq.gz	Fastqsanger.gz
	ERR3930921.fastq.gz	Fastqsanger.gz
	ERR3930922.fastq.gz	Fastqsanger.gz
	ERR3930913.fastq.gz	Fastqsanger.gz
	ERR3930923.fastq.gz	Fastqsanger.gz

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Project description:Gut microbiota of calves (16S rRNA profiling), treated or untreated with florfenicol.

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Project 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 â¥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; Qâ¤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.

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