Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Holstein cattle rumen whole metagenome sequence Madison, WI

PROVIDER: PRJNA507739 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8266640_subreads.fastq.gz	Fastqsanger.gz
	SRR8266650_subreads.fastq.gz	Fastqsanger.gz
	SRR8266660_subreads.fastq.gz	Fastqsanger.gz
	SRR8266641_1.fastq.gz	Fastqsanger.gz
	SRR8266641_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 35

Similar Datasets

Expression analysis of rumen epithelium of cattle during weaning

Project description:Investigation of whole genome gene expression level changes in rumen epithelium of dairy cattle at different stages of rumen development and on different diets.

2009-11-01 | GSE18382 | GEO

Single-cell RNA analyses of cattle ruminal epithelial cells

Project description:Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. Here we present an initial effort of single-cell transcriptomic analyses of cattle ruminal epithelial cells during the rumen development. We obtained 5064 and 1372 cells from Holstein ruminal epithelial cells before and after weaning, respectively. We reported 6 cell types across their temporal and spatial distributions, which were partially correlated with rumen epithelium layer’s structures and functions. We also reported a distinct sets of cell markers for these cell types, for example, CRA1, HMMR, MKI67, and EZH2 for the dividing epithelial cells and the TGFB pathway and the keratin gene family for keratinized epithelial cells. Our proposed a cell lineage model may contribute to the understanding of cattle rumen epithelial proliferation and development.

2021-10-01 | GSE166473 | GEO

Holstein-Friesian Dairy Cattle Rumen

Project description:Holstein-Friesian Dairy Cattle Rumen Raw sequence reads

| PRJNA554894 | ENA

Microbiota-host crosstalk mechanism in the newborn and adult rumen at single-cell resolution

Project description:As the unique organ, rumen plays vital roles in providing products for humans, however, the underlying cell composition and interactions with epithelium-attached microbes remain largely unknown. Herein, we performed an integrated analysis in single-cell transcriptome, epithelial microbiome, and metabolome of rumen tissues to explore the differences of microbiota-host crosstalk between newborn and adult cattle models. We found that fewer epithelial cell subtypes and more abundant immune cells (e.g., Th17 cells) in the rumen tissue of adult cattle. Metabolism-related functions and oxidation-reduction process were significantly upregulated in the adult rumen epithelial cell subtypes. The epithelial Desulfovibrio was significantly enriched in the adult cattle. To further clarify the role of Desulfovibrio in host’s oxidation-reduction process, we performed metabolomics analysis of rumen tissues and found that Desulfovibrio showed a high co-occurrence probability with the pyridoxal in the adult cattle compared with newborn ones. The adult rumen epithelial cell subtypes also showed stronger ability of pyridoxal binding. These indicates that Desulfovibrio and pyridoxal likely play important roles in maintaining redox balance in adult rumen. The integrated analysis provides novel insights into the understanding of rumen function and facilitate the future precision improvement of rumen function and milk/meat production in cattle.

2022-11-17 | GSE183285 | GEO

Whole genome bisulfite sequencing of muscle, liver, brain tissues in cattle

Project description:In this study, we generated whole genome bisulfite sequencing data 3 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues.

2021-12-31 | GSE180592 | GEO

The transcriptomic profile of peripheral blood nuclear cells in bovine and cervine in peak lactation and dry period

Project description:The aim of the study was to identify genes which are differentially expressed in the peripheral blood nuclear cells of two breeds of cattle (Holstein-Friesian and Polish Red) and cervine in different points in their physiological states (dry-off period, peak of lactation) RNA from peripheral blood nuclear cells taken from cattle and cervine in peak lactation and dry period were hybridized to Agilent two color microarrays with a common reference. There were four Holstein-Friesian cattle, four Polish Red cattle and four deer investigated. The whole blood was drawn in two time point from each animal – during dry period and peak lactation. This means that there were six research groups (Holstein-Friesian cattle in dry period and Holstein-Friesian cattle in peak lactation; Polish Red cattle in dry period and Polish Red cattle in peak lactation; Deer in dry period and Deer in peak lactation). Using Gene Spring Software (one-way ANOVA and Tukey's HSD Post-hoc test) three lists of differentially expressed transcripts were obtained: a list of 576 transcripts which differ deer in dry period and in peak lactation, a list of 437 transcripts which differ Holstein-Friesian cattle in dry period and in peak lactation and a list of 158 transcripts which differ Polish Red cattle in dry period and in peak lactation.

2014-02-11 | E-GEOD-54790 | biostudies-arrayexpress

Analyses of methylomes of multiple tissues in cattle

Project description:In this study, we generated whole genome bisulfite sequencing data of 19 samples for 13 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues. In this study, we generated whole genome bisulfite sequencing data of 6 samples for 5 tissues in Hereford cattle. We analyzed the variations of DNA methylation among tissues.

2020-04-30 | GSE147087 | GEO

Characterization and Comparison of the Leukocyte Transcriptomes of Three Cattle Breeds

Project description:In this study, we use mRNA-Seq to characterize and compare the leukocyte transcriptomes of Holstein, Jersey, and Cholistani with respect to variations in sequence, expression, and splicing. Poly A+ RNA are extracted from leukocytes of pools of blood drawn from cows of three different breeds, Holstein, Jersey, and Cholistani. The objective of the study is to compare sequence variation and gene expression of the three cattle breeds.

2013-07-02 | E-GEOD-48487 | biostudies-arrayexpress

Analyses of methylomes of Bones in cattle

Project description:In this study, we generated whole genome bisulfite sequencing data of 2 samples for Bones in Holstein cattle. We analyzed the variations of DNA methylation among tissues compared to other tissues we generated before.

2020-04-30 | GSE147184 | GEO

Project description:Rumen metagenome sequencing of Holstein cattle of 1-4 parity

| PRJNA1071736 | ENA