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Full-length transcriptome sequencing of longissimus dorsi muscle of yak and cattle-yak based on nanopore

ABSTRACT: Full-length transcriptome sequencing of longissimus dorsi muscle of yak and cattle-yak based on nanopore

PROVIDER: PRJNA1120020 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR29278217_subreads.fastq.gz	Fastqsanger.gz
	SRR29278218_subreads.fastq.gz	Fastqsanger.gz
	SRR29278220_subreads.fastq.gz	Fastqsanger.gz

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Full-length transcriptome sequencing of longissimus dorsi muscle of yak and cattle-yak based on nanopore

Project description:Short-reading long RNA sequencing technology has been used to study the transcriptome of skeletal muscle of yak and cattle-yak, but it cannot accurately define full-length transcripts and alternative splicing isoforms. In this study, based on Oxford Nanopore Technologies ( ONT ) full-length sequencing technology, the longissimus dorsi transcription profiles of yak and cattle-yak were obtained. A total of 20323 new genes and 172870 new transcripts were identified, and 159700 new transcripts were successfully annotated. A total of 157812 AS events, 58073 SSRs, 57468 complete ORFs, 2296 transcription factors and 20404 lncRNAs were detected. The analysis found that different structural variations have specific functions, which contribute to the coordination of muscle development and the diversity of gene expression. In addition, the differentially expressed transcripts in longissimus dorsi muscle of yak and cattle-yak were involved in MAPK and JAK-STAT signaling pathway related to muscle development and growth. PPI analysis of differentially expressed transcripts suggested that TNNI2 may play a prominent role in the differences in muscle growth and meat quality traits between yak and cattle-yak. Our study enriched the transcriptome data of yak dorsal muscle and provided a reference for the production of yaks with higher meat yield and better meat quality.

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Proteomics Analysis of Longissimus Dorsi of Cattle-Yak and Yak

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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.

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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.

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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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