Bovine gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA360818 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bos taurus strain:Holstein dairy cows Metagenome
| PRJNA258240 | ENA
Project description:bovine gut metagenome breed:Bos taurus Raw sequence reads
| PRJNA325214 | ENA
Project description:Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 genes have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ~105 Bos taurus indicus X Bos taurus taurus F1 conceptuses using RNA sequencing. For this, we developed a bioinformatics pipeline to identify parental-specific SNPs after filtering A-to-I RNA editing sites. We identified 53 genes subject to monoallelic expression. A total of 23 are genes known to be imprinted in the cow and 7 are previously-characterized imprinted genes in human and/or mouse that have not be reported to be imprinted in cattle. Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinting clusters, whereas the other 13 genes are distributed across the bovine genome and not close to any known imprinting clusters. To exclude potential cis-eQTL effects on allelic expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus X Bos taurus taurus F1s and identified eight novel imprinted genes in bovine. Further, we identified 671 candidate A-to-I RNA editing sites and describe imprinted X inactivation in the bovine trophectoderm-derived CT1 cell line. Our results expand the imprinted gene list in bovine and demonstrate that monoallelic gene expression can be the result of cis-eQTL effect.
2016-08-17 | GSE77389 | GEO
Project description:Bos mutus gastric substance Metagenome
| PRJNA1036001 | ENA
Project description:Bos taurus Raw16S rRNA Amplicon Sequencing Reveals Rumen Microbial Community Structure in 38 Cattle sequence reads
| PRJNA1242574 | ENA
Project description:Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose. We identified over 470 candidate CNV regions (CNVRs) in Bos B. taurus/B. indicus; 118 candidate CNV regions (CNVRs) in B. grunniens, 139 CNVRs in B. bubalis. Furthermore, based on the Y haplotypes of B. taurus/ B. indicus, Wwe also identified 69, 337, and 251 candidate CNV regions (CNVRs) in the sub-groups of Y1, Y2 and Y3 haplotypes.
2014-12-30 | GSE47086 | GEO