Liver and fat transcriptomic changes related to fat content in pigs
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE160436 | GEO | 2020/10/30
REPOSITORIES: GEO
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Project description:The present work emplyed pigs as an animal model for recognition of molecular processes associated with fat deposition. The Transposase-Accessible Chromatin signal changes dependent on fat content were showed at the liver levels. In the experiment Złotnicka White pigs were used that were not under selection pressure, because they are included in to National Preservation Program.
2022-04-03 | GSE199870 | GEO
Project description:Liver and fat transcriptomic changes related to fat content in pigs
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Project description:Intramuscular (i.m.) fat content influencing consumerâs acceptability of pork is considered as a limiting factor for meat quality. To gain insight into the biological basis of individual variability in i.m. fat content, both gene expression profiling and proteomic investigation were associated in pig longissimus muscle (LM). Keywords: intramuscular fat, gene expression, pigs, proteomics, microarray, pork meat Animals were sampled from a population of 1,000 pigs generated as an F2 intercross between two production sire lines: FH016 (Pietrain type, France Hybrides SA, St Jean de Braye, France) and FH019 (Synthetic line, from Duroc, Hampshire and Large White founders, France Hybrides SA, St Jean de Braye, France).
2010-05-07 | E-GEOD-10759 | biostudies-arrayexpress
Project description:Intramuscular (i.m.) fat content influencing consumer’s acceptability of pork is considered as a limiting factor for meat quality. To gain insight into the biological basis of individual variability in i.m. fat content, both gene expression profiling and proteomic investigation were associated in pig longissimus muscle (LM). Keywords: intramuscular fat, gene expression, pigs, proteomics, microarray, pork meat
2009-01-15 | GSE10759 | GEO
Project description:To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels.
2015-01-08 | GSE62696 | GEO
Project description:To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels. Liver mRNA profiles of intact male pigs fed a HFC diet, castrated male pigs fed a HFC diet, and castrated male pigs treated with testosterone fed a HFC diet were generated by deep sequencing, using Illumina HiSeq 2000.
2015-01-08 | E-GEOD-62696 | biostudies-arrayexpress
Project description:Intramuscular fat (IMF) content in pork is an important element of consumer preference, and is positively correlated with meat quality, including tenderness and juiciness. With advances in RNA sequencing technologies, transcriptome-related differences can be associated with specific traits in animals. The objective of this study was to investigate the differentially expressed genes (DEG) closely related with IMF content in porcine longissimus muscle using RNA sequencing. A total of 107 Berkshire pigs were used for IMF content measurements and significant difference between extremely high (H, n=3) and low (L, n=3) IMF content groups was found (P < 0.0001). From multi-dimensional scaling analyses, it was observed that the relationships between H and L groups were similar to each other. Here, we identified a total of 134 genes that were differentially expressed between the groups (FDR < 0.05, and FC ≥ 2). Functional analyses with DEGs revealed that the lipid metabolism (SCD and FASN) was one of the significant biological processes related with IMF content determination. In addition, we also found that DEGs related with muscle regeneration (MYOG and VEGFA) and extracellular matrix (COL1A1, COL1A2, COL5A1, COL14A1, and COL15A1) were changed between individuals with the extreme IMF contents, interestingly. These results will aid in understanding the regulation of IMF contents in pigs.
2017-06-15 | GSE86086 | GEO
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
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. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality. In the present study, we measured the IMF content for 265 crossed pigs of Duroc x Luchuan pigs, from which individuals with extremely high (6.03% ± 0.58%, n = 12) and low (1.67% ± 0.42%, n = 12) IMF contents were selected to identify differentially expressed genes (DEGs) related to IMF content in the longissimus dorsi. RNA sequencing for 24 samples in total identified 312 differentially expressed transcripts that were significantly enriched in triglyceride biosynthesis- and metabolism-related processes (p-value ≤ 0.05 and fold change ≥ 1.5). Functional enrichment analysis revealed that the PPAR signaling pathway was the most significantly enriched pathway (p-value = 0.024, represented by ADIPOQ, FABP3, FABP4, LPL, PLIN4 and SCD). When a more stringent condition was applied (gene-based q-value ≤ 0.2 and fold change ≥ 1.5), only 17 transcripts remained to be differentially expressed, including LEP, ATP6V1F, SDR16C5, TUSC5, MPZ, PRX, PTPN4, BEX1, MVB12B, ZFP62, P4HA2, IDH2, THOC7, KRT14, FCGRT, MYPN and LPL. Among these DEGs, TUSC5 was significantly upregulated in the group of high IMF contents (log2FC = 1.114, p-value = 3.02E-5) and was suspected as a strong new candidate gene affecting porcine IMF content since it was the target gene of PPAR-gamma. The present study provided new data and candidate genes for the genetic study of porcine IMF content.
2023-12-30 | GSE117414 | GEO
Project description:Purpose: Obesity and dyslipidemia are associated with increased risk of renal disease.Testosterone deficiency aggravated high-fat diet-induced obesity and hypercholeterolemia. However,whether testosterone deficiency or testosterone deficiency-induced dyslipidemia aggravate the progression of renal disease is not clear. To gain insight into the role of testosterone in modulating renal lipid metabolism, we profiled renal gene expression by RNA-Seq in HFC-fed intact male pigs (IM), castrated male pigs (CM), and castrated male pigs with testosterone replacement (CMT). Methods: Sexually mature male miniature pigs were either surgical castrated or sham-operated, and castrated with testosterone replacement. We administrated to pigs a high-fat and high-cholesterol (HFC) diet for twelve weeks. RNA-Seq was employed to profile renal gene expression in pigs with different testosterone levels. Conclusions: This study demonstrated that testosterone deficiency aggravated renal lipid accumulation in pigs fed an HFC diet and that these effects could be reversed by testosterone replacement therapy. Impaired metabolic processes, bile acid secretion,estrogen signaling pathway and enhanced triglyceride synthesis may contribute to the increased renal lipid accumulation induced by testosterone deficiency and an HFC diet.
2023-01-17 | GSE125343 | GEO