Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of transcriptome profiles between bulls and steers in the longissimus dorsi muscle of Korean cattle

ABSTRACT: Purpose: The goals of this study are to determine effects of castration on gene expression in longissimus dorsi muscle by comparing transcriptome profiles and to search candidate genes related with beef quality like flavor, tenderness, juiciness and fat deposition Methods: longissimus dorsi muscle mRNA profiles of 3 bulls and 3 steers of Korean cattles were generated by RNA sequencing using Illumina NextSeq 500. After quality checking, Tophat2 software was used for read mapping, and EdgeR was used to identify differentially expressed genes (DEGs) between bulls and steers. Gene ontology pathway analysis on DEGs was conducted with DAVID tool for categorization of DEGs. Results: Using an optimized data analysis workflow, we mapped about 58 million sequence reads per sample to the bovine genome (build UMD3.1) and identified 18,027 expressed genes in the longissimus dorsi muscle of bulls and steers with TopHat2 workflow. RNA-seq data confirmed 1,146 differentially expressed genes (adjusted p-value, FDR <0.05). Conclusions: We comparatively analyzed the transcriptome profile from longissimus dorsi muscle of bulls and steers of Korean cattles using NGS and identified DEGs between bulls and steers. The functional annotation analysis of DEGs found that transcriptome profile difference in longissimus dorsi muscle by castration.

ORGANISM(S): Bos taurus

PROVIDER: GSE95789 | GEO | 2020/03/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome changes following castration of Korean cattle bulls in longissimus dorsi muscle

Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes. A customized bovine Combimatrix microarray containing 10,199 genes were constructed, and transcripome of longissimus dorsi muscle was compared between Korean cattle bulls (3 bulls) and steers (3 high-marbled and 3 low-marbled steers) by using the microarray hybridzation.

2013-06-30 | E-GEOD-35085 | biostudies-arrayexpress

Transcriptome changes following castration of Korean cattle bulls in longissimus dorsi muscle

Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes.

2013-06-30 | GSE35085 | GEO

Bos taurus

Project description:Transcriptome changes following castration of Korean cattle bulls in longissimus dorsi muscle

| PRJNA150917 | ENA

Bos taurus

Project description:Comparison of transcriptome profiles between bulls and steers in the longissimus dorsi muscle of Korean cattle

| PRJNA378406 | ENA

Transcriptional response of muscle tissue to a high energy feeding regimen in Japanese Black and Holstein steers

Project description:Microarray gene expression profiling to identify differentially regulated genes in Musculus longissimus dorsi (MLD) of Japanese Black (JB) steers compared to Holstein steers (HS)

2015-12-02 | GSE75348 | GEO

Identification of a circulating miRNA that is involved in meat yield and connects exosomes and longissimus dorsi muscle in Korean cattle steers

Project description:MicroRNAs (miRNAs) regulate gene expression. The aim of this study was to identify circulating miRNAs that are involved with meat yield and connect exosomes and longissimus dorsi (LD) muscle in Korean cattle steer. Thus, we performed analyses of the carcass characteristics, exosome extraction, bovine miRNA array, mature miRNA qPCR, bioinformatics, and qPCR. Our analysis of the carcass characteristics relative to the yield grade (YG) showed that the yield index (YI) and rib eye area were the highest, whereas the backfat thickness was the lowest for YG A cattle among the three YGs. We performed a miRNA microarray and a Venn diagram analysis to sort the circulating miRNAs that connect exosomes and LD muscle. Mature miRNA qPCR showed that miR-15a (r = 0.84), miR-26b (r = 0.91), and miR-29c (r = 0.92) had positive relationships with exosomes and LD muscle. In YG A cattle, miR-26b was considered to be a circulating miRNA connecting exosomes and LD muscle because the expression pattern of miR-26b was similar in the microarray and miRNA qPCR for miR-26b-targeted genes, where the expression levels of DIAPH3 and YOD1 were lower than those in YG C cattle. Our results suggest that circulating miR-26b may participate in cell maintenance by regulating DIAPH3 and YOD1 in the LD muscle of Korean cattle. 29 or 30 month Korean cattle steers were classified by yield grade(YG) A, B, and C. miRNA expression patterns for exosome and LD muscle were compared among YGs.

2016-03-01 | E-GEOD-73389 | biostudies-arrayexpress

Microarray Analysis on the Differences of Gene Expression in Longissimus Dorsi Muscle Tissue between 1-month and 24-month Chinese Red Steppes

Project description:In order to establish the correlation between biological processes and the mechanisms of gene expression controlling beef traits formation in bovine, microarray analysis was performed to capture the differences in gene expression related to beef traits profile in Longissimus Dorsi muscle tissue between 1-month and 24-month Chinese Red Steppes. 1282 (5.6%) probes showed significant differences at the two stages in the experiment, and 1008 differential gene annotations were obtained using Capitalbio molecule annotation system. BLAST analysis revealed that 1001(78.1%) probe genes shared significant similarity in amino acid sequence with other functional genes (As of June 2009). 126 genes showing strong correlation with beef traits were gained by the GO analysis. With the KEGG analysis, 63 pathways were found to be related to beef traits which involved 73 genes. 28 genes were found in a single pathway, while 35 genes were found in 2-16 pathways respectively. The panels of transcripts and gene pathways analysis in different growth stages may be helpful for the study on beef traits formation, and the gene expression profile construction in Longissimus Dorsi muscle tissues, would make a foundation for screening candidate genes which have genetic effect on meat quality in bovine. Keywords: Microarray analysis; Beef traits; Differences of gene expression; Longissimus Dorsi muscle tissue; Chinese Red Steppe A total of 18 bulls of the same breed (Chinese Red Steppe) were included in the study; 9 were 1month old while another 9 were 24 months old and were provided by Jilin Academy of Agricultural Sciences. They were maintained in standard conditions and fed with standard diet. The bulls were humanely killed at the slaughter house of the academy, and fresh longissimus dorsi muscle tissues were obtained during slaughter, immediately frozen in liquid nitrogen and stored at -80M-BM-0C for microarray analysis.

2013-06-01 | E-GEOD-21782 | biostudies-arrayexpress

Identification of circulating miRNA involved in meat yield of Korean cattle

Project description:Cattle plays an important role in providing essential nutrients through meat production. Thus, we focused on epigenetic factors associated with meat yield. To investigating circulating miRNAs that are involved with meat yield and connect biofluids and longissimus dorsi (LD) muscle in Korean cattle, we performed analyses of the carcass characteristics, miRNA array, qPCR, and bioinformatics. Carcass characteristics relative to the yield grade (YG) showed that the yield index and rib eye area were the highest, whereas the backfat thickness was the lowest for YG A (equal to high yield grade) cattle among the three YGs. miRNA array sorted the circulating miRNAs that connect biofluids and LD muscle. miRNA qPCR showed that miR-15a (r = 0.84), miR-26b (r = 0.91), and miR-29c (r = 0.92) had positive relationships with biofluids and LD muscle. In YG A cattle, miR-26b was considered to be a circulating miRNA connecting biofluids and LD muscle because the target genes of miR-26b was more involved with myogenesis. Then, miR-26b targeted genes, DIAPH3 and YOD1 were downregulated in YG A cattle. Our results suggest that miR-15a, miR-26b, and miR-29c are upregulated in biofluids and LD muscle whereas, downregulation of DIAPH3 and YOD1 in the LD muscle of finishing cattle steers.

2016-03-01 | GSE73389 | GEO

Supranutritional Maternal Organic Selenium Supplementation During Different Trimesters of Pregnancy in Beef Cattle

Project description:We used an RNA-Seq transcriptomic approach to investigate Longissimus dorsi muscle gene expression profiles of calves from cows receiving weekly Se-yeast boluses at supranutritional concentrations during different trimesters of gestation. Pregnant beef cows received, except the control group (CTR), weekly supranutritional selenium-yeast boluses (105 mg Se/wk) during the first (TR1), second (TR2), or third (TR3) trimester of gestation. Within 12 to 48 h of birth, muscle samples were collected from the Longissimus dorsi using a Bergstrom biopsy needle (inner diameter: 5 mm). Muscle biopsies were placed into sterile vials, stored on ice and frozen at – 80 ºC until total RNA isolation was performed. After sequencing and read quality control, we identified 3,048 unique differentially expressed genes (DEGs) across all group comparisons (FDR < 0.05 and |log2FC| > 1.5). Furthermore, we predicted 237 unique transcription factors that putatively regulate the DEGs. Our findings suggest a beneficial effect of supranutritional maternal organic Se supplementation during late gestation on Se-status and muscle development and function of newborn calves.

2022-12-30 | GSE189456 | GEO

Proteomic analysis of the Longissimus dorsi muscle of Wannanhua pigs

Project description:4D-Label-free quantitative proteomic analysis of the longissimus dorsi muscle tissue of the Wannanhua pig during the rapid fat deposition stage (120d and 240d)

2024-01-26 | PXD046675 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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