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RNA-seq of longissimus dorsi muscles in Japanese black (Wagyu) and Chinese Red Steppes cattle

ABSTRACT: RNA-seq of longissimus dorsi muscles in Japanese black (Wagyu) and Chinese Red Steppes cattle

PROVIDER: PRJNA680176 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13107018_1.fastq.gz	Fastqsanger.gz
	SRR13107018_2.fastq.gz	Fastqsanger.gz
	SRR13107019_1.fastq.gz	Fastqsanger.gz
	SRR13107019_2.fastq.gz	Fastqsanger.gz
	SRR13107020_1.fastq.gz	Fastqsanger.gz

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RNA-seq of longissimus dorsi muscles in Japanese black (Wagyu) and Chinese Red Steppes cattle

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Whole Genome Bisulfite Sequencing of Longissimus Dorsi Muscles between Japanese Black (Wagyu) and Chinese Red Steppes Cattle

Project description:We performed a comparative genome-wide methylation analysis of longissimus dorsi muscles between the Japanese Black (Wagyu) and Chinese Red Steppes cattle, which exhibit significant differences in meat quality traits. This will allow us to better understand the correlation between DNA methylation variants and meat quality traits.

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Expression data from longissimus dorsi muscle of Meishan pigs

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Effects of maternal nutrient restriction during pregnancy on the adult offspring longissimus dorsi transcriptome in cattle

Project description:Maternal undernutrition during pregnancy followed by ad libitum access to nutrients during postnatal life induces postnatal metabolic disruptions in multiple species. As skeletal muscle is a major metabolic organ, RNAseq was performed on the longissimus dorsi muscles of slaughter-weight adult females that had been exposed to nutrient-restriction in utero.

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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

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

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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

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

Project description: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.

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