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The expression profiles of longissimus dorsi muscle from six Laiwu pigs (three with extremely high and three with extremely low intramuscular fat content).

ABSTRACT: The expression profiles of longissimus dorsi muscle from six Laiwu pigs (three with extremely high and three with extremely low intramuscular fat content).

PROVIDER: PRJNA854631 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19909239_1.fastq.gz	Fastqsanger.gz
	SRR19909239_2.fastq.gz	Fastqsanger.gz
	SRR19909240_1.fastq.gz	Fastqsanger.gz
	SRR19909240_2.fastq.gz	Fastqsanger.gz
	SRR19909241_1.fastq.gz	Fastqsanger.gz

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The expression profiles of longissimus dorsi muscle from six Laiwu pigs (three with extremely high and three with extremely low intramuscular fat content).

Project description:To understand the role of message RNA (mRNAs, lncRNAs and circRNAs) in regulation of intramuscular fat deposition, the expression profiles of longissimus dorsi muscle from six Laiwu pigs were sequenced based on rRNA-depleted library construction. We then performed gene expression profiling analysis using data obtained from RNA-seq.

2022-08-31 | GSE207279 | GEO

Integrative analysis of transcriptomics and proteomics of Longissimus dorsi muscle to identify proteins underlying intramuscular fat content in pigs

Project description:The Laiwu pig is famous for its excessively higher level of IMF content, however, the exact regulatory mechanism is still unknown. The intramuscular fat content (IMF) is an economically important traits in pigs, which is controlled by multiple genes and biological pathways. In the present study, we performed an integrated transcriptome-assisted label-free quantitative proteomic analysis of longissimus dorsi (LD) muscle in Laiwu pigs at the fastest IMF deposition stage. A total of 5074 unique proteins were identified and 191 were differentially abundant proteins (DAPs) (> 1.2-fold cutoff, p < 0.05), which were hierarchically clustered in the LD muscle over two developmental stages from 120 d to 240 d. Proteins participating in the regulation of lipolysis in adipocytes and AMPK signaling pathway were identified. Six proteins were analyzed using parallel reaction monitoring (PRM) to confirm the reliability of the TMT proteomic analysis. Association networks of differentially abundant proteins revealed that these DAPs were mainly involved in ribosome biosynthesis in eukaryotic species. A comparasion between transcriptomic (mRNA) and proteomic data revealed seven differentially expressed genes corresponding to DAPs. This study, for the first time, provides some data for the elucidation of the molecular mechanism of IMF deposition in pigs.

2020-01-09 | PXD011718 | Pride

RNA-seq Analysis of the Longissimus Muscle of Laiwu and Yorkshire Pigs

Project description:Intramuscular fat (IMF) content is the determining factor for meat taste. To reveal the genetic basis of IMF content, genetic studies have made some progress in lean-type pig breeds, but fewer studies have been conducted in Chinese fat-type pigs. We selected Laiwu and Yorkshire pigs as models, and transcriptomic analysis was conducted on the longissimus dorsi muscle to investigate the gene expression patterns linked to high and low intramuscular fat (IMF) content. The purpose of the study was to determine the differences in intramuscular fat between the two breeds and identify the reasons for the differences. To further systematically investigate the potential biologic significance of phenotype divergence, the identified DEGs were annotated into multiple pathways based on KEGG bioinformatic databases (P < 0.05). According to the identified DEGs, the results revealed a number of enriched pathways in AMPK signaling pathway, cAMP signaling pathway, PPAR signaling pathway, and so on. Functional enrichment analysis showed that PPARγ, ADIPOQ, LEP, LIPE, SCD, FABP4 and PLIN1 were represented.

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Comparative DNA Methylation analysis reveals genes regulating adipogenesis in Laiwu pigs over two developmental stages

Project description:We performed DNA methylation analysis of the longissimus dorsi (LD) muscle between two development stages (120 and 240 days after birth) in Laiwu pigs, an indigenous fatty pig breed in North China. This study provides a reference for exploring methylation regulation mechanisms affecting fat deposition in obese pigs.

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Transcriptome profiling of the intramuscular fat content in Longissimus dorsi between Angus and Chinese Simmental cattle

Project description:The intramuscular fat (IMF) content of different beef cattle breeds varies greatly, which plays an important role in taste and nutritional value. However, the molecular mechanism of fat metabolism and deposition in beef cattle is still not very clear. In this study, the meat quality traits of Angus cattle and Chinese Simmental cattle were compared, the transcriptome of the longissimus dorsi muscle (LD) between Angus cattle and Chinese Simmental cattle was then analyzed to identify key genes related to fat metabolism and adipogenesis by high-throughput RNA-seq technology. In the current study conducted a comprehensive analysis on the transcriptome of the longissimus dorsi muscle (LD) of Angus and Simmental cattle, and identified differentially expressed genes related to lipid metabolism，which may have a great impact on on the formation of IMF.

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Comparative transcriptome analysis reveals genes regulating myogenesis and adipogenesis in Laiwu pigs over four developmental stages

Project description:We performed transcriptome analysis of the longissimus dorsi (LD) muscle during four development stages (60, 120, 240 and 400 days after birth) in Laiwu pigs, an indigenous fatty pig breed in North China. This study provides a reference for exploring transcriptome regulation mechanisms affecting muscle growth and development in obese pigs.

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Transcriptome Profiling of Longissimus Dorsi Muscle of Donkeys with High and Low Intramuscular Fat Content

Project description:The content of intramuscular fat (IMF) is closely related to meat quality traits. In this study, in order to explore the candidate genes related to IMF content, the longissimus dorsi muscle of Guangling donkey was measured for intramuscular fat content. According to its intramuscular fat content, it was divided into two groups, the low fat group (L , N=3) and high-fat group (H, n=3), using RNA-seq to identify differentially expressed genes (DGEs) on the longissimus dorsi muscle tissue of Guangling donkey with high and low intramuscular fat content to reveal the possibility Gene network and metabolic pathways that help increase intramuscular fat content. A total of 167 DEGs (|log2Fold Change|>=1 and FDR<0.05) were detected in the high (H) and low (L) groups of Guangling donkeys, of which 64 were up-regulated genes and 103 were down-regulated genes. The GO enrichment and KEGG pathway analysis showed that these differential genes were enriched in several biological processes and pathways related to adipocyte differentiation, lipid biosynthesis, and neutral lipid metabolism. These results will help to further explore the molecular mechanism of IMF deposition in donkeys and provide a theoretical basis for the molecular breeding of Guangling donkeys.

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Expression data from Northeastern Indigenous and Large White longissimus dorsi

Project description:To understand the molecular basis of distinct pork quality in Chinese indigenous and Western breed, longissimus dorsi samples were collected from three adult Northeastern Indigenous and from three adult Large White. Total RNA was extracted and subjected to porcine Affymetrix Genechip. The study helps to elucidate the genetic mechnism of divergent pork quality and provide the theory basis for selection and genetic improvement of meat quality traits in porcine. Six longissimus dorsi samples were collected from three Northeastern Indigenous and from three Large White. Three Large White were control samples. Total RNA was extracted from each sample.Gene-expression profiling was performed for each RNA sample separately on the GeneChipÂ® Porcine Genome Array at CapitalBio Corporation (Beijing, China).

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Expression data from Northeastern Indigenous and Large White longissimus dorsi

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