Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative transcriptomic analysis of subcutaneous adipose tissue from local pig breeds

ABSTRACT: The aim of this work was to explore the genome function of AL and BI pig breeds to better understand the underlying physiological mechanisms associated with body fat accretion and lean muscle tissue deposition and therefore, meat quality of these breeds. Dorsal subcutaneous fat samples were collected at slaughter from adult AL and BI pigs (n=4 for each genotype) with ~150kg body weight. Total RNA was obtained and sequenced for transcriptome analysis and a bioinformatic analysis using the DESeq2 R package was implemented. A total of 458 differentially expressed genes (q-value<0.05) were identified, with 263 found overexpressed in AL and 195 in BI, including 47 novel genes. Several key genes involved in de novo fatty acid biosynthesis, elongation and desaturation were consistently found upregulated in AL such as acly, fasn, me1, elovl6 and scd. A functional enrichment analysis of the candidate genes was performed using Ingenuity Pathway Analysis, which revealed GH signalling, HOTAIR regulatory pathway, AMPK and IGF-1 signalling among the top canonical pathways associated to the BI. Potential upstream regulators such as SCAP, MED1, SREBF2 and PPARG were found activated in AL, suggesting increased adipogenesis and cholesterol synthesis. Regulators found in the BI included INSIG1, INSIG2 and FOXO1 associated with lipogenesis inhibition, and MEF2C and PDGFB, related to myogenesis, cell proliferation and differentiation.

ORGANISM(S): Sus scrofa

PROVIDER: GSE145956 | GEO | 2020/05/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Muscle transcriptome profile of Alentejano and Bísaro pig breeds

Project description:Gene expression is one of the main factors to influence meat quality by modulating fatty acid composition and deposition rates in the muscle tissue. This study aimed to explore the transcriptomic universe of the longissimus lumborum muscle in two local pig breeds with distinct genetic background (n=10) using next-generation sequencing technologies and the traditional Real-Time qPCR. RNAseq yielded 49 DEG’s, with 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. MYH3 was found significantly overexpressed (log2 FC=-1.191, q<0.05) in the leaner BI pigs and is suggested to impact the development of skeletal muscle tissue. Several candidate genes for lipid metabolism with low counts excluded with RNAseq such as ACLY (p<0.05), ADIPOQ (p<0.01), ELOVL6 (p<0.001), LEP (p<0.05) and ME1 (p<0.05) showed to have an unavoidable relevance through Real-Time quantitation. These results agree with the more adipogenic profile of the AL breed. Adiponectin resistance and higher levels of MAP3K14 may explain an induced insulin resistance, increased inflammatory response and lower loin size.

2021-03-01 | GSE159817 | GEO

INSIG1 in NASH pathophysiology and in the hepatic wound-healing response

Project description:We investigated the biological function of INSIG1 in acute (CCl4) and chronic (NASH) liver damage. Male whole-body Insig1 wild-type (WT), Heterozygous (HET) and Knock-out (KO) mice were: 1) challenged with Olive Oil or CCl4 single IP injection and sacrificed 4 days after the treatment; 2) fed Low Fat Diet (LFD) or Western Diet plus Sugar Water (WDSW) and sacrificed after 12 weeks of the challenge. Hepatic RNA was extracted and studied by Next Generation Sequencing to highlight changes in the transcriptome driven by the challenges and genotype-associated differences.

2021-04-14 | E-MTAB-9864 | biostudies-arrayexpress

Quantitative phosphoproteomic analysis reveals the regulatory networks of elovl6 on lipid and glucose metabolism in zebrafish

Project description:Elongation of very long-chain fatty acids protein 6 (Elovl6) has been reported to be associated with clinical treatments of a variety of metabolic diseases. However, there is no systematic and comprehensive study to reveal the regulatory role of Elovl6 in the mRNA, protein and phosphorylation levels. We established the first knock-out (KO), elovl6-/-, in zebrafish. Compared with wild type (WT) zebrafish, KO presented significant higher content of whole-body lipid and lower content of fasting blood glucose. We utilized RNA-Seq, tandem mass tag (TMT) labeling-based quantitative technology, and LC-MS/MS to perform the transcriptomic, proteomic, and phosphoproteomic analyses of livers from WT and elovl6-/- zebrafish. There were 734 differentially expressed genes (DEG) and 559 differentially expressed proteins (DEP) identified out of quantifiable 47251 transcripts and 5525 proteins between elovl6-/- and WT zebrafish. Meanwhile, 680 differentially expressed phosphoproteins (DEPP) with 1054 sites were found out of quantifiable 1230 proteins with 3604 sites. GO and KEGG analysis of the transcriptomic and proteomic data further suggested that the abnormal lipid metabolism and glucose metabolism in KO were mainly related to fatty acid degradation and biosynthesis, glycolysis/gluconeogenesis and PPAR signaling pathway. In the phosphoproteomics, some phosphoproteins and kinases critical for lipid metabolism and glucose metabolism, including ribosomal protein S6 kinase (Rps6kb), mitogen-activated protein kinase14 (Mapk14), and V-akt murine thymoma viral oncogene homolog 2, -like (Akt2l), were identified. These results allowed us to catch on the regulatory networks of elovl6 on lipid and glucose metabolism in zebrafish. To our knowledge, this is the first multi-omic study of zebrafish lacking elovl6, which provides strong datasets to better understand many lipid/glucose metabolic risks posed to human health.

2020-05-27 | PXD017702 | Pride

Inhibition of S6K lowers age-related inflammation and immunosenescence and increases lifespan via the endolysosomal system

Project description:The nutrient-sensing Target of Rapamycin complex 1 (TORC1) is an evolutionarily conserved regulator of longevity. S6 kinase (S6K) is an essential downstream mediator for the effect of TORC1 on longevity. However, mechanistic insights on how TORC1-S6K signalling promotes lifespan and healthspan are still limited. Here we show that activity of S6K in the Drosophila fat body is essential for rapamycin-mediated longevity. Fat-body-specific activation of S6K blocked lifespan extension upon rapamycin feeding and induced accumulation of multilamellar lysosomal enlargements. Besides, fat body-specific S6K knockdown extended lifespan in files. We performed proteomics for Drosophila fat body to explore the fat body-specific regulation of protein expression by two separate datasets: fat body-specific S6K activation (Lsp2GS>S6KCA) with rapamycin treatment; and fat body-specific S6K inhibition (Lsp2GS>S6KRNAi). To assess if the age-prolonging mechanisms of TORC1-S6K signalling are conserved between flies and mammals, we assessed the impact of rapamycin treatment in the proteome of liver from C3B6F1 mice (F1 hybrids of C3H/HeOuJ females and C57Bl/6N males).

2024-01-12 | PXD035293 | Pride

Expression data from D.melanogaster larvae with a constitutively active Imd in the fat body

Project description:Activation of innate immune responses in the Drosophila larval fat body affects the physiological host responses. In order to characterize the effect of the activated immune responses in the fat body on the Drosophila, we used whole-genome microarray analysis and found that activation of the immune deficieny pathway (Imd) in the fat body alters the transcriptional profiles of Drosophila larvae. As we expected many of genes involved in regulation of antimicrobial peptides were upregulated in the larvae with elevated Imd activity in the fat body. Notably, we found activatioan of Imd in the fat body negatively affects expression of genes involved in glycolysis, energy production and insulin signaling pathway. Overall, our analysis showed that activation of innate immune signaling in the larval fat body significantly affects cellular pathways that regulate metabolism.

2018-01-24 | GSE109470 | GEO

Dataset on fat body proteome of Anopheles stephensi Liston

Project description:Fat body is an important tissue in the context of vitellogenesis, vector immunity, vector physiology and vector-parasite interaction. However, the proteome of this vital organ has not been investigated in any Anopheline species so far. In this study, we employed multiple fractionation method followed by high resolution mass spectrometry to characterize fat body proteome of female mosquitoes An. stephensi Indian strain. In all, we identified 4, 535 proteins in the fat body and a subset of these proteins were found to be restricted to fat body. Gene ontology analysis of these proteins suggested their role in metabolism, lipid transport, vitellogenesis, mosquito immunity and oxidation-reduction processes. By far, this is the largest proteomic resource of fat body in any mosquito species.

2019-01-07 | PXD006677 | Pride

Hepatic transcriptome profiling of liver-specific Elovl6 knockout mice fed a high-sucrose diet

Project description:Elovl6 is a member of mammalian fatty acid elongase that is responsible for converting C16 saturated and monounsaturated fatty acids into C18 species. To understand the role of Elovl6 in liver, we generated liver-specific Elovl6 knockout mice (Albumin-Cre;Elovl6 fl/fl C57BL/6J). The goal of this experiment was to determine effects of hepatocyte Elovl6 deficiency on the murine liver transcriptome under lipogenic condition.

2019-09-20 | GSE123494 | GEO

Suckling lamb perirenal fat transcriptome

Project description:The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf= 8, Churra= 6) was used for the RNA-Seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes. The differential expression analysis performed identified 373 differentially expressed genes (DEGs) between the two compared breeds. In Assaf lambs, DEGs were enriched in Gene Ontology (GO) biological processes related to fatty-acid oxidation, while in Churra lambs, the majority of the significantly enriched GO terms were related to cholesterol synthesis, which suggests that upregulated DEGs in Assaf lambs are implicated in fat burning, while the Churra upregulated DEGs are linked to fat accumulation.

2018-07-18 | GSE108314 | GEO

RNA-seq analysis in adipocytes that lack APPBP2 and/or PRDM16

Project description:We systematically determined the extent to which APPBP2 loss stimulate beige adipocyte biogenesis in a PRDM16-dependent fashion. To this end, we ran RNA-seq analysis in adipocytes that lack APPBP2 and/or PRDM16. By overlapping the transcriptome data with published dataset of brown/beige fat (Chondronikola et al., 2016; Perdikari et al., 2018; Shinoda et al., 2015a), we found that APPBP2 loss significantly increased 72 genes whose expression was enriched in brown adipocytes relative to white fat. Among 72 brown/beige fat-enriched genes, we found that 90.28% (65/72 genes) of them were regulated in a PRDM16-dependent manner. The data suggest that PRDM16 is required for the majority, if not all, of APPBP2’s action on brown fat genes

2022-06-06 | GSE196699 | GEO

TMT-based proteomic analysis of CSF in dogs with intervertebral disc herniation

Project description:In our study, MS-based high-resolution proteomic analysis of CSF have been employed in order to gain deeper insights into changes occurring during IVDH in dogs, monitoring the pathophysiological processes at the protein and metabolite levels. The proteomics study involved canine patients classified within two groups. Healthy dogs (control group) (N=6) were mix breeds (20 kg average body weight), age 2-6 years, while the intervertebral disc herniation group (N=9) were mixed breeds (body weight 6-15 kg), age 7-12 years. In IVDH dogs, disc herniation was detected in T13/L1/L2 discs by CT. The dogs in IVDH group were paraplegic with preserved deep pain reflex and underwent a surgery procedure for decompression of the spinal cord.

2021-11-25 | PXD024921 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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