DNA sequencing of Israeli Holstein bulls
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB59761 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10906942_1.fastq.gz | Fastqsanger.gz | |||
| ERR10906942_2.fastq.gz | Fastqsanger.gz | |||
| ERR10906943_1.fastq.gz | Fastqsanger.gz | |||
| ERR10906943_2.fastq.gz | Fastqsanger.gz | |||
| ERR10906944_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 66 |
Similar Datasets
Project description:The aim of this study was to investigate the effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose in Holstein-Friesian bulls and possible downstream effects on reproduction. Holstein Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were assigned to either a high (n=10) or low (n=10) plane of nutrition. Calves were fed in order to achieve an overall growth rate of 1.08 and 0.5 kg/day for the high and low plane of nutrition treatments, respectively. At 126 days of age, the bulls were euthanized using an intravenous overdose of sodium pentobarbitone and subcutaneous adipose tissue samples were harvested and RNAseq analysis was performed. At the end of the trial period, there were 745 genes differentially expressed in adipose tissue of bulls on the high plane of nutrition relative to those on the low plane of nutrition (P<0.05; FDR<0.05; fold change >2.0). Plane of nutrition altered the expression of genes involved in energy production and branched chain amino acid degradation. Plane of nutrition was also found to down regulate genes such as leptin and adiponectin which are known to effect reproductive function. This study identifies some of the molecular mechanisms regulated by feeding bulls a high plane of nutrition, which may be incorporated into future breeding programmes for artificial insemination centres.
2018-04-12 | GSE97674 | GEO
Project description:The aim of this study was to investigate the effect of early calf-hood nutrition on the transcriptomic profile of the arcuate nucleus of the hypothalamus, the anterior pituitary and the testes in Holstein-Friesian bulls and possible downstream effects on reproduction. Holstein Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were assigned to either a high (n=10) or low (n=10) plane of nutrition. Calves were fed in order to achieve an overall growth rate of 1.2 and 0.5 kg/day for the high and low plane of nutrition treatments, respectively. At 126 days of age, the bulls were euthanized using an intravenous overdose of sodium pentobarbitone and arcuate nucleus of the hypothalamus, anterior pituitary and the parenchyma of the testes tissue samples were harvested and RNAseq analysis was performed. At the end of the trial period,
2018-04-12 | GSE97673 | GEO
Project description:The aim of this study was to examine changes in the mRNA transcriptional profile of spermatozoa in Holstein-Friesian bulls. Spermatozoa from bulls divergent for feritlity status were used for this study with 10 High fertility bulls and 10 Low fertility bulls. RNA was extracted and subsequently subjected to miRNAseq analysis. 6 miRNA were identified as differentially expressed in the spermatozoa between bulls of high and low feritlity status.
2022-09-13 | GSE198043 | GEO
Project description:The aim of this study was to examine changes in the miRNA transcriptional profile of spermatozoa in Holstein-Friesian bulls. Spermatozoa from bulls divergent for feritlity status were used for this study with 10 High fertility bulls and 10 Low fertility bulls. RNA was extracted and subsequently subjected to miRNAseq analysis. 13 miRNA were identified as differentially expressed in the spermatozoa between bulls of high and low feritlity status.
2022-09-13 | GSE196750 | GEO
Project description:Pre-pubertal Holstein bull calves fed a higher plane of nutrition had larger testes, earlier puberty, higher serum LH, testosterone and greater sperm production potential than those fed a restricted diet. In addition, pre-pubertal calves fed a high-nutrition diet had higher IGF-I and more proliferating and differentiating Sertoli cells much earlier in life, compared to those fed normal or low-nutrition diets. The objective was to determine changes in mRNA expression of genes in the testes of bulls fed either a high or low pre-pubertal diet. Holstein bull calves maintained on either a high (20% crude protein (CP) and 71.6% Total Digestible Nutrients (TDN)) or low (12% CP and 64.4% TDN) diet from 2 wk of age, were castrated at 8, 16, 24 and 32 wk and testicular mRNA extracted and sequenced. Differential expression of genes mainly occurred at 16 and 24 wk, with minor changes detected at 32 wk. At 16 wks, functional analysis of DE mRNA with DAVID revealed the common biological processes enriched to be "cholesterol" and "fatty acid biosynthesis" with majority of the genes including HMGCR, HMGCS1, HSD17 being upregulated in high-diet bulls (P<0.05). Major pathways enriched at 16 wks were "cholesterol biosynthesis", "steroid metabolism" and "activation of gene expression by Sterol regulatory element-binding protein (SREBP)" (P<0.05). Mature Sertoli cell marker Connexin 43, was upregulated at 16 wk, whereas an immature Sertoli cell marker, AMH was downregulated at 24 wk, in the high-diet group. Network analysis using IPA, revealed an indirect interaction between insulin family receptor and most upregulated cholesterol biosynthesis genes, implying regulation of testicular function. Thus, enhanced pre-pubertal nutrition in Holstein bulls enhanced testicular cholesterol/steroid biosynthesis and Sertoli cell maturation to promote early reproductive development.
2019-05-15 | GSE125082 | GEO
Project description:Recent studies have documented the profound impact of pre-pubertal nutrition on reproductive performance in bulls. Previously, a high plane of nutrition during calfhood (2-30 wk) in beef and dairy bulls hastened puberty explained by an increase in the level of reproductive hormones (LH, testosterone and IGF-I) pre-pubertally, compared to bulls fed less than recommended amounts of energy and protein with no apparent effect on sperm function evaluated by traditional techniques. In addition, upregulated steroid biosynthesis and Sertoli cell maturation was identified in the testicular tissue of high diet bulls at 16 and 24 weeks, respectively. The objective of this study was to evaluate the post- pubertal testes for responses to high (20.0% CP, 67.9% TDN), medium (17.0% CP, 66.0% TDN) and low (12.2% CP, 62.9% TDN) diets fed from 2-30 wk of life. Based on RNA sequencing data, 497 genes were differentially expressed in high vs low diet and 2961 genes in high vs medium diet (P<0.1). According to KEGG analysis, oxidative phosphorylation and ribosome pathways were upregulated in the high diet group (vs medium and low) with majority of the upregulated genes encoding for essential subunits of complex I, III, IV and V of OXYPHOS pathway. In addition, mitochondrial translation, mitotic nuclear division and cell division were enriched in the high vs medium diet group. Supporting the above, the percentage of sperm exhibiting loss of mitochondrial function was lower in the high diet compared to the medium diet (P<0.1). Thus, enhanced early life nutrition upregulated mitochondrial function in both the testes and sperm of post-pubertal Holstein bulls.
2020-01-01 | GSE137690 | GEO
Project description:The objective of this study was to examine changes in muscle gene expression of growing bulls during a period of dietary energy restriction followed by a period of subsequent realimentation and compensatory growth. Purebred Holstein Friesian bulls (n=20) were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=10) followed by ad libitum access to feed for a further 55 days or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=10). The first 125 days of the trial were denoted as Peirod 1, during which treatment groups were fed differentially. The subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependnet on each treatment group. Muscle biopsies were collected at 2 time points (end of the differential feeding in Period 1 (d 120) and during the realimentation phase in Period 2 (d 15 of re-alimentation). RNA was extracted and muscle gene expression was examined using RNAseq technology and bioinformatic analysis. During the differential feeding period, over-represented pathways including fatty acid beta oxidaiton, oxidative phosphorylation and TCA cyclewere identified, which indicate utilisation of lipid sotes for energy utilisaiton and also alterations in energy produciton during dietary restriciton in muscle. During the realimentation period, pathways involved in energy produciton were over-represented, with the direction of fold changes opposite to that of these pathways in Period 1. additionally, a number of genes involved in cell division and cellular proliferation were up-regulated during compensatory growth in re-alimentation, thereby promoting accelerated cell growth and proliferation in muscle tissue of animals experiencing compensatory growth. This information can be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction. 40 muscle RNA samples were analysed in total. 10 samples were from muscle biopsies collected at the end of a period of dietary restriction (d 120) and 10 samples were from muscle biopsis collected during the initial stages of compensatory growth (d 15 of re-alimentation). In addition, RNA was also anlaysed from 10 samples collected from animals fed a libitum at each of these two timepoints.
2015-09-04 | E-GEOD-64289 | biostudies-arrayexpress
Project description:The objective of this study was to examine changes in hepatic gene expression of growing bulls during a period of dietary energy restriction followed by a period of subsequent realimentation and compensatory growth. Purebred Holstein Friesian bulls (n=20) were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=10) followed by ad libitum access to feed for a further 55 days or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=10). The first 125 days of the trial were denoted as Peirod 1, during which treatment groups were fed differentially. The subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependnet on each treatment group. At the end of each period, 10 animals from each treatment group (10, restricted fed and 10 ad libitum fed) were slaughtered and hepatic tissue collected within thirty minutes of slaughter. RNA was extracted and hepatic gene expression was examined using RNAseq technology and bioinformatic analysis. During the differential feeding period, over-represented pathways including amino acid and lipid metabolism, protein synthesis and cell cycle/proliferation were identified, which indicate alterations in metabolic and growth rate in the liver during dietary restriction . During the realimentation period, pathways involved in cell cycle and cell growth as well as protein synthesis were over-represented, with the direction of fold changes opposite to that of these pathways in Period 1. This information can be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction.
2016-12-20 | GSE64285 | GEO
Project description:The objective of this study was to examine changes in muscle gene expression of growing bulls during a period of dietary energy restriction followed by a period of subsequent realimentation and compensatory growth. Purebred Holstein Friesian bulls (n=20) were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=10) followed by ad libitum access to feed for a further 55 days or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=10). The first 125 days of the trial were denoted as Peirod 1, during which treatment groups were fed differentially. The subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependnet on each treatment group. Muscle biopsies were collected at 2 time points (end of the differential feeding in Period 1 (d 120) and during the realimentation phase in Period 2 (d 15 of re-alimentation). RNA was extracted and muscle gene expression was examined using RNAseq technology and bioinformatic analysis. During the differential feeding period, over-represented pathways including fatty acid beta oxidaiton, oxidative phosphorylation and TCA cyclewere identified, which indicate utilisation of lipid sotes for energy utilisaiton and also alterations in energy produciton during dietary restriciton in muscle. During the realimentation period, pathways involved in energy produciton were over-represented, with the direction of fold changes opposite to that of these pathways in Period 1. additionally, a number of genes involved in cell division and cellular proliferation were up-regulated during compensatory growth in re-alimentation, thereby promoting accelerated cell growth and proliferation in muscle tissue of animals experiencing compensatory growth. This information can be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction.
2015-09-04 | GSE64289 | GEO
Project description:Pregnancy rates for elite bulls used in artificial insemination (AI) can vary significantly and therefore the identification of molecular markers for bull fertility and targets to improve bull selection is important. β-defensins are peptides with diverse regulatory roles in sperm function across multiple species. To explore the functional impact of DEFB103 CNV on the uterine response in vivo, 18 heifers were inseminated with sperm from bulls categorized by low, intermediate, and high CN levels. Transcriptomic analysis of uterine tissue collected 12 hours after insemination revealed significant differential expression of 58 genes (FDR<0.1) related to sperm migration, immune signaling, and chemotaxis. These findings highlight the significant role of DEFB103 CN in both sperm function and the uterine response to bull sperm, suggesting its potential influence on pregnancy outcomes in cattle.
2024-09-15 | E-MTAB-14398 | biostudies-arrayexpress