Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A multi-tissue atlas of regulatory variants in cattle

ABSTRACT: Genotype?Tissue Expression atlas of cattle using 7,180 publicly available RNA-sequencing (RNA-seq) samples

INSTRUMENT(S): -

ORGANISM(S): Bos Taurus

SUBMITTER: Roslin institute

PROVIDER: PRJEB59574 | EVA | 2023-02-10

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Similar Datasets

E-GTEX-8

Project description:The Genotype-Tissue Expression (GTEx) project v8

2024-12-20 | E-GTEX-8 | ExpressionAtlas

E-MTAB-8022

Project description:RNA-seq of blood samples from bovines immunized with a multicomponent recombinant vaccine against cattle tick.

2020-01-06 | E-MTAB-8022 | ExpressionAtlas

E-MTAB-2836

Project description:RNA-seq of coding RNA from tissue samples of 122 human individuals representing 32 different tissues

2025-01-23 | E-MTAB-2836 | ExpressionAtlas

E-GEOD-41804

Project description:Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype

2025-01-24 | E-GEOD-41804 | ExpressionAtlas

E-MTAB-1733

Project description:RNA-seq of coding RNA from tissue samples of 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes

2025-01-23 | E-MTAB-1733 | ExpressionAtlas

E-MTAB-8135

Project description:Global gene expression profiles of 10 gastric cancer (GC) samples and 10 gastric normal adjacent tissue (gNAT) samples

2025-01-16 | E-MTAB-8135 | ExpressionAtlas

Functional genomics of cattle through integration of multi-omics data

Project description:The cattle industry is the largest of the agricultural commodities in the United States and generated over $101 billion in farm cash receipts during 2016; 28% of all US farm cash receipts. Although the sequence of the bovine reference genome has been publicly available since 2009, annotation of functional genome elements is largely incomplete, resulting in limitations for exploiting the genome to phenome relationship. This project generate high-quality detailed transcript and miRNA status datasets from a comprehensive set of bovine tissues, developmental stages, and cells through a set of rationally selected assays.

2022-07-30 | E-MTAB-11699 | biostudies-arrayexpress

E-MTAB-3579

Project description:RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice tissue in RIKEN FANTOM5 project

2015-06-27 | E-MTAB-3579 | ExpressionAtlas

Transcriptome profiling of muscle by RNA-Seq reveals significant digital gene expression profiling differences between Angus and Luxi Cattle

Project description:The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA-Seq to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in both Chinese Luxi and Angus beef cattle. More than 9,243,921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (FDR≤0.001 AND |log2Ratio|≥1). Among the DGEs, we determined that 147 genes were down-regulated and 85 genes were up-regulated. GO and Pathway analysis were performed to analyze the biological role of the DGEs and determine their contribution to the differences seen in muscle growth and development between local Chinese Luxi cattle and the introduced Angus cattle. This article suggests that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our result provides unprecedented resolution of mRNAs that are expressed across the two breeds.

2014-11-14 | GSE57327 | GEO

Transcriptome profiling of muscle by RNA-Seq reveals significant digital gene expression profiling differences between Angus and Luxi Cattle

Project description:The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA-Seq to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in both Chinese Luxi and Angus beef cattle. More than 9,243,921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (FDRM-bM-^IM-$0.001 AND |log2Ratio|M-bM-^IM-%1). Among the DGEs, we determined that 147 genes were down-regulated and 85 genes were up-regulated. GO and Pathway analysis were performed to analyze the biological role of the DGEs and determine their contribution to the differences seen in muscle growth and development between local Chinese Luxi cattle and the introduced Angus cattle. This article suggests that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our result provides unprecedented resolution of mRNAs that are expressed across the two breeds. Three Luxi and three Angus cattle that were eighteen months of age were generated by RNA-Seq

2014-11-14 | E-GEOD-57327 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data