Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33343740_1.fastq.gz | Fastqsanger.gz | |||
| SRR33343740_2.fastq.gz | Fastqsanger.gz | |||
| SRR33343741_1.fastq.gz | Fastqsanger.gz | |||
| SRR33343741_2.fastq.gz | Fastqsanger.gz | |||
| SRR33343742_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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.
2016-08-19 | E-GEOD-76841 | biostudies-arrayexpress
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 ≥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.
2016-08-19 | GSE76841 | GEO
Project description:The aim of the overall study was to investigate the development of immune competence in artificially reared dairy calves and in two breeds of naturally suckled beef calves over the first 168h of life. Dairy calves were fed 5% total body weight of colostrum, with beef calves monitored to ensure natural ingestion of colostrum. Blood samples were taken from all calves at 24h 48h 72h and 168h, and analysed for alterations to immunes genes.
2018-10-29 | GSE114432 | GEO
Project description:Choline is a vital micronutrient that can be utilized in the formation of betaine and multiple phospholipids. In this study, we aimed to confirm, and expand on previous findings, how choline impacts embryos from the first 7 days of development to affect postnatal phenotype. Bos indicus embryos were cultured in a choline-free medium or medium supplemented with 1.8 mM choline. Blastocyst-stage embryos were transferred into crossbred recipients. Once born, calves were evaluated at birth, 94 d, 178 d and at weaning (average age=239 d). Following weaning, all calves were enrolled into a feed efficiency trial before being separated by sex, with males being slaughtered at approximately 580 d of age and females followed until their first pregnancy check. Results confirm that exposure of 1.8 mM choline chloride during the first 7 d of development alters postnatal characteristics of the resultant calves. Calves of both sexes from choline-treated embryos were consistently heavier through weaning. Males had heavier testes at 3 mo of age. There were sex-dependent alterations in DNA methylation in whole blood caused by choline treatment. After weaning, feed efficiency was affected by an interaction with sex, with choline calves being more efficient for females and less efficient for males. Calves from choline-treated embryos were heavier, or tended to be heavier, than calves from control embryos at all observations after weaning. Carcass weight was heavier for choline calves and the cross-sectional area of the Longissumus dorsi muscle was increased by choline. Few females became pregnant during the experiment although numerically more choline females were pregnant than control females. Results confirm that exposure of the preimplantation embryo to 1.8 mM choline altered phenotypes of the animal through the first 19 months after birth.
2025-09-22 | GSE262304 | GEO
Project description:Bacterial succession in the gut of pre-weaning dairy calves
| PRJNA399771 | ENA
Project description:Background: Weaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq. Results: The leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling, were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating that a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling. Conclusions: This study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long-term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress. Examination of a time course (day 0, 1, 2 and 7) for 2 treatments, calves either housed with their dam (control) or housed and simultaneously weaned, using RNA-seq. The supplementary processed data file 'read_counts.txt' contains unnormalized read counts for each Ensembl bovine gene in each of the 48 samples. Unnormalized counts are required for input to EdgeR. Genome build: Btau4.0
2012-06-25 | E-GEOD-37447 | biostudies-arrayexpress
Project description:The impact of postnatal heat stress exposure in neonatal calves is not well-understood, and adequate heat abatement methods during the pre-weaning phase are lacking. This study aimed to investigate the impact of pre-weaning heat stress on liver gene expression profiles.
2023-03-19 | GSE227323 | GEO
Project description:The impact of postnatal heat stress exposure in neonatal calves is not well-understood, and adequate heat abatement methods during the pre-weaning phase are lacking. This study aimed to investigate the impact of pre-weaning heat stress on liver DNA methylation profiles.
2023-03-19 | GSE227249 | GEO
Project description:Assessing Faecalibacterium prausnitzii as a Psychobiotic in Pre-weaning Dairy Calves
| PRJNA1085263 | ENA
Project description:Pre-weaning heat stress alters liver DNA methylation in dairy calves
| PRJNA944647 | ENA