GEO DataSets

(Submitter supplied) Large/abnormal offspring syndrome (LOS/AOS) is a congenital overgrowth syndrome reported in ruminants produced by assisted reproduction (ART-LOS) which exhibit global disruption of the epigenome and transcriptome. LOS/AOS shares phenotypes and epigenotypes with the human congenital overgrowth condition Beckwith-Wiedemann syndrome. We have reported that LOS occurs spontaneously (SLOS), however, to date, no study has been conducted to determine if SLOS has the same methylome epimutations as ART-LOS. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24230

38 Samples

Download data: BEDGRAPH

(Submitter supplied) In this study, we generated whole genome bisulfite sequencing data 4 tissues in cattle. We analyzed the variations of DNA methylation among tissues.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL15749 GPL24230

9 Samples

Download data: TXT

(Submitter supplied) The goal was to examine and compare the transcriptomic profiles of fully differentiated 15 month old muscle derived from bulls belonging to different breeds and showing different performance.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL11648

4 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24230

25 Samples

Download data: TXT

(Submitter supplied) In this study, we generated 94 RNA-seq data that were colloced from different tissues in Hereford cow (L1 Dominette 01449) and its relatives. By combining these RNA-seq data with our other data and published data, we uniformly assembled and analyzed a total of 723 transcriptomes from 91 tissues and cell types in cattle, to identify tissue-specific genes with the highest specific expression. We then detected the trait-relevant tissues and cell types, and improved genomic prediction for milk production traits.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15749

94 Samples

Download data: TXT

(Submitter supplied) To further our understanding of bovine fat depot biology we screened 5 discrete fat depots (IMF, intermuscular, omental, kidney and subcutaneous) for patterns of genome-wide gene expression

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL11649

96 Samples

Download data: TXT

(Submitter supplied) We reported the bovine pituitary gland gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24980

18 Samples

Download data: ZIP

(Submitter supplied) We reported the bovine liver gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24980

18 Samples

Download data: ZIP

(Submitter supplied) In this study, 7188 bovine skeletal muscle lncRNAs were identified by RNA-Seq and a stringent screening procedure in four different muscle tissues. These lncRNAs shared many characteristics with other mammalian lncRNAs, such as the shorter ORF and lower expression level than mRNAs. Furthermore, the chromosomal locations and global expression patterns for these lncRNAs were also described in detail.Our results provided a global expression pattern of lncRNAs specific to bovine skeletal muscle and supplied us important targets for studying the function of lncRNAs in muscle development, which would help to better identify mechanisms underlying muscle development in bovine.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19172

4 Samples

Download data: TXT

(Submitter supplied) Structural and functional impacts of copy number variations (CNVs) on livestock genomes are not yet well understood. In this study, we have identified 1853 CNV regions (CNVRs) using population-scale sequencing data generated from 75 cattle of 8 breeds (Holstein, Angus, Jersey, Limousin, Romagnola, Brahman, Gir and Nelore). Individual genome sequence coverage ranged from 4 to 30 fold, with a mean of 11.8 fold. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11314

25 Samples

Download data: BED, PAIR

(Submitter supplied) Background: A comprehensive transcriptome survey, or "gene atlas", provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and 3 cattle cell lines. Results: The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the bovine genome accounting for 85% of the total raw tag abundance. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9323

95 Samples

Download data

(Submitter supplied) Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, are currently being associated with phenotypes of clinical relevance, mostly in humans and mice. Notwithstanding, little is known about the extent of CNV that contributes to genetic variation in cattle. This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9220 GPL9221 GPL9219

114 Samples

Download data: PAIR

(Submitter supplied) Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9866 GPL9865

90 Samples

Download data: PAIR, TXT