Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circular RNA Expression and Regulation Profiling in Testicular Tissues of Immature and Mature Wandong Cattle (Bos taurus)

ABSTRACT: Wandong cattle are an autochthonous Chinese breed used extensively for beef production. The breed tolerates extreme weather conditions and raw feed and are resistant to tick-borne diseases. However, the genetic basis of testis development and sperm production as well as breeding management is not well established in local cattle. In this study, we performed total RNA-Seq and comprehensively analyzed the circ-RNA expression profiling of the testes samples of six bulls at 3 years and 3 months of developmental age. In total, 17 013 circ-RNAs were identified, of which 681 circRNAs (P-adjust < 0.05) were differentially expressed (DE). Among these DE circ-RNAs, 579 were upregulated and 103 were downregulated in calf and bull testes. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the identified target genes were classified into three broad functional categories, including biological process, cellular component, and molecular function, and were enriched in the lysine degradation, cell cycle, and cell adhesion molecule pathways.

ORGANISM(S): Bos taurus

PROVIDER: GSE183347 | GEO | 2021/09/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling of monocytes derived from tolerant (Sahiwals, Bos indicus) and susceptible (Holstein-Friesians, Bos taurus) cattle to in vitro infection with Theileria annulata

Project description:Tropical theileriosis in a cattle disease of global economic importance, caused by the tick-borne protozoan parasite Theileria annulata. Conventional control strategies are failing to contain the disease and an attractive alternative is the use of pre-existing genetic resistance or tolerance. However, tropical theileriosis tolerant cattle are less productive than some susceptible breeds. To combine resistance and production traits requires an understanding of the mechanisms involved in resistance. Therefore, we have compared the response of monocytes derived from tolerant (Sahiwals, Bos indicus) and susceptible (Holstein-Friesians, B. taurus) cattle to in vitro infection with T. annulata. Over 150 genes exhibited breed-specific differential expression during the course of infection and nearly one third were differentially expressed in resting cells, implying that there are inherent differences between monocytes from the breeds. Fifty sequences currently only match ESTs or are unique to the library used to generate the microarray. The differential expression of a selection of genes was validated by quantitative RT-PCR, e.g. CD9, prion protein and signal-regulatory protein alpha. A large proportion of the differentially expressed genes encode proteins expressed on the plasma membrane or in the extracellular space and cell adhesion was one of the major Gene Ontology biological processes identified. We therefore hypothesise that the breed-specific tolerance of Sahiwal cattle compared to Holstein-Friesians is due to the interaction of infected cells with other immune cells, which influences the immune response generated against T. annulata infection. The BoMP microarray is available from the ARK-Genomics facility (www.ark-genomics.org).

2007-04-26 | E-MAXD-25 | biostudies-arrayexpress

Bos taurus

Project description:Coat color dilution in Kumamoto sub-breed of Japanese Brown cattle

| PRJDB14144 | ENA

Bos taurus breed:cattle

Project description:Bos taurus breed:cattle Raw sequence reads

| PRJNA846691 | ENA

Bos taurus breed:cattle

Project description:Bos taurus breed:cattle Raw sequence reads

| PRJNA846867 | ENA

Transcriptome profiling and Co-expression networks of longissimus dorsi muscle in Gayal（Bos frontalis）and Banna cattle（Bos taurus） with different beef qualities

Project description:The Gayal (Bos frontalis) is a rare semi-domesticated cattle in China. Gayal has typical beef body shape and good meat production performance. Compared with other cattle species, it has the characteristics of tender meat and extremely low fat content. To explore the underlying mechanism responsible for the differences of meat quality between different breeds, the longissimus dorsi muscle (LM) from Gayal and Banna cattle (Bos taurus) were investigated using transcriptome analysis. The gene expression profiling identified 638 differentially expressed genes (DEGs) between LM muscles from Gayal and Banna cattle. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the gene products were mainly involved in the PPAR signaling pathway, lipid metabolism and amino acid metabolism pathway. Protein-protein interaction（PPI） network analysis showed APOB, CYP7A1, THBS2, ITGAV, IGFBP1 and IGF2R may have great impact on meat quality characteristics of Gayal. Moreover, three transcription factors, FOXA2, NEUROG2, and RUNX1, which may affect meat quality by regulating the expression of genes related to muscle growth and development have also been found. In summary, our research reveals the molecular mechanisms that cause Gayal meat quality characteristics. It will contribute to improving meat quality of cattle through molecular breeding.

2024-09-01 | GSE164462 | GEO

Bos taurus

Project description:MIRA-Seq analysis of bovine dermal fibroblasts isolated from two breeds of cattle, Holstein (dairy breed) and Angus (beef breed).

| PRJNA292866 | ENA

Bos taurus breed:Mongolian cattle

Project description:Bos taurus breed:Mongolian cattle Genome sequencing

| PRJNA1011026 | ENA

Bos taurus breed:Wandong Cattle

Project description:Bos taurus breed:Wandong Cattle Genome sequencing

| PRJNA1066093 | ENA

Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle.

Project description:The Toll-like receptor (TLR) and peptidoglycan recognition protein 1 (PGLYRP1) genes play key roles in the innate immune systems of mammals. While the TLRs recognize a variety of invading pathogens and induce innate immune responses, PGLYRP1 is directly microbicidal. We used custom allele-specific assays to genotype and validate 220 diallelic variants, including 54 nonsynonymous SNPs in 11 bovine innate immune genes (TLR1-TLR10, PGLYRP1) for 37 cattle breeds. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and we were unable to differentiate between the specialized B. t. taurus beef and dairy breeds, despite an average polymorphism density of one locus per 219 bp. Ninety-nine tagSNPs and one tag insertion-deletion polymorphism were sufficient to predict 100% of the variation at all 11 innate immune loci in both subspecies and their hybrids, whereas 58 tagSNPs captured 100% of the variation at 172 loci in B. t. taurus. PolyPhen and SIFT analyses of nonsynonymous SNPs encoding amino acid replacements indicated that the majority of these substitutions were benign, but up to 31% were expected to potentially impact protein function. Several diversity-based tests provided support for strong purifying selection acting on TLR10 in B. t. taurus cattle. These results will broadly impact efforts related to bovine translational genomics.

| S-EPMC2806759 | biostudies-literature

Bos taurus genome assembly.

Project description:BackgroundWe present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque.ResultsThe assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information.Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly.ConclusionThe biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research.

| S-EPMC2686734 | biostudies-literature

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