Gene expression data from longissimus dorsi muscle 25-day-old male pigs
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE87599 | GEO | 2016/10/05
SECONDARY ACCESSION(S): PRJNA345348
REPOSITORIES: GEO
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Project description:To characterize the mechanism of porcine skeletal muscle development, transcriptome analysis of longissimus dorsi muscle between Shaziling and Yorkshire pig breeds
2016-06-23 | GSE70673 | GEO
Project description:To characterize the mechanism of porcine skeletal muscle development, transcriptome analysis of longissimus dorsi muscle between Shaziling and Yorkshire pig breeds Three male Shaziling pigs and three male Yorkshire pigs from two full-sibs families at 25-days old were slaughtered
2016-06-23 | E-GEOD-70673 | biostudies-arrayexpress
Project description:Western commercial pig breeds have been intensively selected, resulting in a sizeable, rapid, and efficient accretion of muscle but a reduction in meat quality. When compared with Western commercial pig breeds, Chinese indigenous pig breeds exhibited slower growth rates and reduced lean meat content but superior perceived meat quality. To study the factors that determine meat quality, we examined piglets of one Western commercial breed (Yorkshire) and one Chinese indigenous breed (Wannanhua) and sequenced the longissimus dorsi muscle using RNA-sequencing (RNA-seq). We analyzed their transcriptomes, focusing on identifying candidate genes that may influence porcine muscle growth, meat quality and adipose deposition. Gene ontology functional enrichment and pathway enrichment analyses identified differentially expressed genes primarily associated with glycolytic metabolism, biological processes of muscle development and signaling pathways related to fatty acid metabolism, growth and carcass traits. This finding suggests that the differentially expressed genes may play important roles in determining meat quality traits. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) confirmed the differential expression of twelve selected differentially expressed genes. This study identified a number of novel candidate genes for porcine meat quality and carcass traits that merit further investigation to elucidate the molecular mechanisms responsible for muscle growth and fat deposition.
2015-11-30 | GSE75045 | GEO
Project description:Intramuscular fat (IMF) content is an important trait closely correlated with meat quality, which is highly variable among swine breeds from diverse genetic backgrounds. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA-sequencing to detect transcriptome in the longissimus dorsi muscle of Wei pigs (a Chinese indigenous breed) and Yorkshire pigs (a Western lean-type breed) with different IMF content. A total of 717 differentially expressed genes (DEGs) were identified in our study, with 323 up-regulated and 394 down-regulated genes in Wei pigs compared with Yorkshire pigs. GO analysis showed that DEGs significantly related to muscle proliferation and development, lipid storage and catabolic, extracellular matrix structural constituent, and neutral amino acid transmembrane transporter activity. Pathway analysis revealed that DEGs associated with fatty acid metabolism, steroid biosynthesis, glycerophospholipid metabolism, protein digestion and absorption, and amino acid metabolism. Quantitative real time PCR confirmed the differential expression of 11 selected DEGs from both pig breeds. The results provide useful information to investigate the transcriptional profiling in skeletal muscle of different pig breeds with divergent phenotypes, and several DEGs can be taken as functional candidate genes for affecting pork quality.
2017-05-20 | GSE99092 | GEO
Project description:4D-Label-free quantitative proteomic analysis of the longissimus dorsi muscle tissue of the Wannanhua pig during the rapid fat deposition stage (120d and 240d)
2024-01-26 | PXD046675 | Pride
Project description:Purpose: MicroRNAs (miRNAs) are non-coding small miRNA ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and theses difference are programmed during prenatal muscle development.To shed directly light on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds. Methods: skeletal musle miRNA profiles of Meishan pig and large white pig were generated by deep sequencing, in triplicate, using Illumina Hiseq2000 . The sequence reads that passed quality filters were analyzed at the mature miRNA level . qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We measure the myofiber phenotypes of LW and MS at developmental stages of 35, 55 and 90 days post-conception (dpc). Results shows that the myogenesis process is more intense in MS than in LW at 35 dpc. To investigate the role of miRNAs involved in regulating muscle development at earlier stages of myogenesis and decipher the miRNAs transcriptome difference between LW and MS, here, the miRNAomes of longissimus dorsi muscle collected at 35 dpc from female LW and MS were analyzed by deep sequencing. Overall, we identified 1147 unique miRNAs comprising 434 known miRNAs, 239 conserved miRNAs and 474 candidate miRNAs. Expression analysis of the 10 most abundant miRANs in every library indicated that functional miRNAome may be smaller and tend to be highly expressed. These set of miRNA may play house keeping roles that were involved in myogenesis. A total of 87 miRNAs were significantly differentially expressed between LW and MS (reads > 1000, P < 0.05). Gene ontology (GO) and KEGG pathway enrichment analysis revealed that the differentially expressed miRNAs (DE miRNAs) were associated mainly with muscle contraction, WNT, mTOR, and MAPK signaling pathways. In addition, the expression patterns of myomiRs (miR-1,-133,-206) at three prenatal stages (35,55 and 90 dpc) were determined using qRT-PCR, Notably, ssc-miR-133 was significantly more highly expressed in LW pig skeletal muscle at all prenatal stages compared with its expression in LW pig skeletal muscle. We concluded that the higher expression levels of miR-133 in MS, possibly regulated by myoD, are potential strategies for improvement of myogenesis in earlier prenatal stages. Conclusions: our results add new information to existing data on porcine miRNAs and be helpful to investigate the dominant (main functional) muscle-related miRNAs sets in different pig breeds. In addition, this study provide a profound knowledge on the role of miRNAs in prenatal muscle development, which could provide great reference value for pork quality improvement.
2017-08-31 | GSE88860 | GEO
Project description:One of the most important determinants of meat quality is the intramuscular fat content (IMF). The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the current study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq technique allowed identifying in the samples analyzed around 10,000 of the 25,878 annotated genes. In addition to this, the 42.46% of the identified transcripts corresponded to newly predicted isoforms. The differential expression analyses revealed a total of 221 DE annotated genes and 116 DE newly isoforms. Functional analyses identified an enrichment of overexpressed genes in animals with a higher content of IMF involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC and ADIPOQ) and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB and SEMA4D) in the groups of animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. On the one hand, co-expression networks analyses revealed six lncRNAs (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1 and CIDEC. The computation of the regulatory impact factors (RIFs) revealed a total of 301 transcriptionally regulatory factors involved in the expression differences, some of them have a role in adipogenesis (ARID5B, CREB1, VDR, ATF6 and SP1) and other ones take part of myogenesis and development of skeletal muscle (ATF3, KLF11 and MYF6). The results obtained provide a relevant insight about the knowledge of the genetics mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors is proposed for a further identification of polymorphisms susceptible of integrate in a selection program.
2018-07-12 | GSE116951 | GEO
Project description:This study takes pig longissimus dorsi muscle as the object. Through spatial transcriptome research, we clarified the gene expression distribution of different types of muscle fibers in the tissue, and their corresponding marker genes were identified.
2022-05-17 | GSE203094 | GEO
Project description:The skeletal muscle growth and development is a very complicated but precisely regulated process with interwoven molecular mechanisms. Skeletal muscle is a very heterogeneous tissue that is made up of a large variety of functionally diverse fiber types. Muscle mass is therefore largely determined by the number and size of those fibres. These fibre characteristics are determined by hyperplasia before birth and by hypertrophy after. Around 65 dpc and three postnatal stages (newborn, 3 days; young, 60 days; and mature, 120 days) are key time points in swine skeletal muscle growth and development. We used microarrays to detail the global programme of gene expression underlying porcine skeletal muscle growth and development. Porcine longissimus dorsi muscles were selected at four stages of development for RNA extraction and hybridization on Affymetrix microarrays. We sought to investigate the global gene expression patterns accompanying the skeletal muscle development. To that end, we selected longissimus dorsi muscles at four time-points: 65 days post coitus, 3 days, 60 days and 120 days afterbirth.
2011-07-01 | E-GEOD-24689 | biostudies-arrayexpress
Project description:The objective of this study was to identify key genes associated with porcine muscle growth and adipose metabolism which different expression in porcine longissimus dorsi muscle tissue between Fat Type Pig(Taihu pig) and Lean Type Pig (Landrace), among developmental phases(Month 0,1,2,3,4,5). The gene expression analyses will increase understanding of impact factors of pork quality by identifying key genes and pathways controlling longissimus dorsi muscle development. Relative real-time RT-PCR was used to confirm differential expression of 5 different expression genes(PPARGC1A, RYR1, IGF2, IGF1R and IGFBP5) which normalized by 3 housekeep genes(ACTB, TBP and TOP2B). Keywords: time course and breed comparison
2008-12-16 | GSE7857 | GEO