Whole transcriptome and miRNAome analysis of porcine muscle tissue in terms of muscle growth and development
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ABSTRACT:
PROVIDER: PRJNA430156 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6495700.fastq.gz | Fastqsanger.gz | |||
| SRR6495701.fastq.gz | Fastqsanger.gz | |||
| SRR6495692.fastq.gz | Fastqsanger.gz | |||
| SRR6495702.fastq.gz | Fastqsanger.gz | |||
| SRR6495693.fastq.gz | Fastqsanger.gz |
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Project description:Whole transcriptome and miRNAome analysis of porcine muscle tissue in the terms of muscle growth and development
| PRJNA419312 | ENA
Project description:Purpose: The aim of present research was to identify miRNAs potentially related with muscle growth in pig Methods: miRNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire. Based on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The miRNA libraries were constructed form total RNA with the use Neb Next Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the protocol. The quantification of obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies) and a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). The miRNA-seq was performed in 36 single-end cycles on HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Differentially expressed microRNAs were detected using the DESeq2 software while validation was performed by qPCR. Results: miRNA-seq approach allowed to identify 196 known and 149 potentially novel miRNAs in both breeds. The comparison of miRNA profiles between pig groups with different loin weight showed differential expression of 57 microRNAs for Hampshire pigs and 34 miRNAs for Pietrain pigs. Furthermore, 18 common microRNAs with differential expression were identified for both breeds tested. The Gene Ontology analysis (DIANA mirPath v.3 tool) confirmed that detected genes were involved in regulation of cell cycle, fatty acid biosynthesis, regulation of actin cytoskeleton, lysine degradation and ubiquitin mediated proteolysis. According to the KEGG Database, these DE miRNAs enrich the following pathways, i.a.: the Hippo signaling pathway, TGF-beta signaling pathway and PI3K-Akt signaling pathway. Conclusions: Obtained results allow to propose the panel of miRNAs, which can be related with porcine muscle growth and development. Such analysis can be the basis of future research in terms of identification of candidate miRNAs related with important production traits in pigs.
2018-04-23 | GSE109215 | GEO
Project description:Purpose: The aim of present research was to identify genes potentially related with muscle growth in pig Methods: RNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire. Base on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The cDNA libraries were constructed form 300 ng of total RNA with the use TruSeq RNA Sample Prep Kit v2 kit (Illumina) according to the protocol. The quantification of obtained libraries was performed on Qubit 2.0 (Invitrogen, Life Technologies) and TapeStation 2200 (D1000 ScreenTape; Agilent). The RNA-seq was performed in 101 single-end cycles on HiScanSQ platform (Illumina) with the use of ruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Each library was sequences in 4 technical replications. The DEGs were detected using DESEq2 software and validation was performed by qPCR. Results: RNA-seq approach allowed to identify 627 and 416 DEGs between pig groups with different loin weight (pvalue <0.05; fold change≤1.5) for Pietrain and Hampshire; respectively. Next, the comparison of obtained genes sets showed 43 genes identified in both breeds. The Gene Ontology analysis (Panther software) confirmed that detected genes were involved in regulation of metabolic process (18 genes), developmental growth or skeletal system development (PCOLCE; BBS2; TBX2; RBBP6; ATAF5). According to David software these genes belong to PI3K-Akt signaling, Focal adhesion and ECM-receptor interaction pathways. Conclusions: Obtained results allow to propose the panel of genes, which can be related with porcine muscle growth and development. Such analysis can be the basis of future research in terms of identification of candidate genes related with important production traits in pigs.
2017-12-01 | GSE107207 | GEO
Project description:Solexa/Illumina deep sequencing was used to obtain miRNA transcriptome profiles for control (basal diet, 14.49% crude protein, 13.73 MJ/kg digestible energy, 0.86% available lysine) and traditional Chinese medicine formula (basal diet+2.5 g/kg traditional Chinese medicine formula) groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed using DAVID functional annotation to identify the biological process function of the miRNAs identified as being involved in muscle fiber regulation. We detected 269 mature miRNAs and 14 pre-miRNAs in the porcine muscle samples, of which 211 were previously unreported. Pathway analyses suggested that several independent signaling pathways were involved in the biological process, cellular component, and molecular function categories, with metabolic pathways showing the most enrichment and including some pathways involved in the regulation of muscle fiber phenotype such as mitogen-activated protein kinase (MAPK), mammalian target of rapamycin, and citrate cycle signaling pathways. Thirty-seven miRNAs exhibited normalized expression of over 10,000 reads per million, accounting for 85.91% of the overall counts of the total porcine mature miRNAs. Among these, 9 were muscle-related miRNAs involved in muscle development, including skeletal satellite cell (ssc)-miR-133a-3p, ssc-miR-486, ssc-miR-26a, ssc-miR-21, ssc-miR-1, ssc-miR-10b, ssc-miR-181a, ssc-miR-128, and ssc-miR-23a. In particular, miR-1 and miR-133 are muscle-specific miRNAs, termed myomiRs, which play an important role in muscle differentiation and development. Furthermore, porcine skeletal satellite cell transfection experiments indicated that overexpression or inhibition of ssc-miR-27a repressed or increased, respectively, MYH7 gene and protein expression through the PGC-1-MEF2C pathway, suggesting that miR-27a participated in the regulation of muscle fiber in skeletal muscle. In conclusion, these miRNAome profiles provide novel insight into the mechanism underlying muscle fiber regulation.
2017-04-07 | GSE80069 | GEO
Project description:We set up a pilot study using Affymetrix Gene Chip® Porcine Genome Arrays to evaluate the impact of time lags from death on gene expression profiling of porcine skeletal muscle at four post mortem time points (up to 24 hrs) during the routine processing of fresh tights
2011-01-19 | GSE26701 | GEO
Project description:Porcine satellite cells play a vital role in the construction, development, and self-renewal of skeletal muscle. In this study, porcine satellite cells were exposed to mimic viral infection poly (I:C) during proliferation and differentiation phases at 0h, 12h, 24h and 48h time points. The untreated and treated porcine satellite cells during proliferation and differentiation phases were further analyzed by RNA sequencing technology. In the proliferation and differentiation phases of porcine satellite cells grown under poly (I:C), 88, 119, 104 and 95 genes were differentially expressed in 0h – 12h treated, 12h – 24h treated, 0h – 24h treated and 24h – 48h untreated comparison libraries, respectively. The GO terms analysis results showed that in the proliferation phase of treated porcine satellite cells, the up-regulated genes related to the immune system were highly expressed. In addition, the gene expression associated with muscle structure development, response to growth factor emerged in the differentiation phase of untreated porcine satellite cells. The biological pathways associated with Influenza A, Toll-like signaling as well as chemokine signaling were revealed through poly (I:C) stimulation of porcine satellite cells. The differentially expressed genes were confirmed by quantitative real-time PCR. Our findings expanded the understanding of gene expression and signaling pathways about the infiltrated mechanism of the virus into porcine skeletal muscle satellite cells.
2018-03-31 | GSE112527 | GEO
Project description:Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content. The comparison was performed between whole gene expression and miRNA profiles of muscle tissue collected from two sire-line pig breeds (Pietrain, Hampshire). The RNA-seq approach allowed the identification of 627 and 416 differentially expressed genes (DEGs) between pig groups differing in terms of loin weight between Pietrain and Hampshire breeds, respectively. The comparison of miRNA profiles showed differential expression of 57 microRNAs for Hampshire and 34 miRNAs for Pietrain pigs. Next, 43 genes and 18 miRNAs were selected as differentially expressed in both breeds and potentially related to muscle development. According to Gene Ontology analysis, identified DEGs and microRNAs were involved in the regulation of the cell cycle, fatty acid biosynthesis and regulation of the actin cytoskeleton. The most deregulated pathways dependent on muscle mass were the Hippo signalling pathway connected with the TGF-β signalling pathway and controlling organ size via the regulation of ubiquitin-mediated proteolysis, cell proliferation and apoptosis. The identified target genes were also involved in pathways such as the FoxO signalling pathway, signalling pathways regulating pluripotency of stem cells and the PI3K-Akt signalling pathway. The obtained results indicate molecular mechanisms controlling porcine muscle growth and development. Identified genes (SOX2, SIRT1, KLF4, PAX6 and genes belonging to the transforming growth factor beta superfamily) could be considered candidate genes for determining muscle mass in pigs.
| S-EPMC5979540 | biostudies-literature
Project description:Background While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy. Results Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks. Conclusions In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.
2010-05-05 | GSE21628 | GEO
Project description:We set up a pilot study using Affymetrix Gene Chip® Porcine Genome Arrays to evaluate the impact of time lags from death on gene expression profiling of porcine skeletal muscle at four post mortem time points (up to 24 hrs) during the routine processing of fresh tights Post mortem skeletal muscle samples were obtained from three commercial hybrid pigs of female sex (of about 160 kg each) raised in the same commercial farm and slaughtered under normal conditions at the same abattoir within 1 minute of each other after stunning by CO2 (concentration 87%) using a dip lift system (Butina, Denmark). A portion of semimembranosus muscle (3-5 g) was sampled from the left legs at 20 minutes (T0) after death following the normal operation of the abattoir. Other samples were collected from the same muscle at the same position after 2 (T1), 6 (T2) and 24 (T3) hrs post mortem in the same abattoir following the cold chain at the abattoir until 4 °C. After sampling, tissues were snap frozen in liquid nitrogen and stored at -80 °C till RNA extraction.
2011-01-19 | E-GEOD-26701 | biostudies-arrayexpress
Project description:Function of the porcine TRPC1 gene in myogenesis and muscle growth
| PRJNA675023 | ENA