Ontology highlight
ABSTRACT:
PROVIDER: PRJNA552780 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9645040.fastq.gz | Fastqsanger.gz | |||
| SRR9645041.fastq.gz | Fastqsanger.gz | |||
| SRR9645042.fastq.gz | Fastqsanger.gz | |||
| SRR9645043.fastq.gz | Fastqsanger.gz | |||
| SRR9645044.fastq.gz | Fastqsanger.gz |
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Project description:Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context. Eleven small RNA libraries from eight adipose tissues, two skeletal muscle tissues and cardiac muscle of pig were sequenced.
2012-05-16 | E-GEOD-30334 | biostudies-arrayexpress
Project description:Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context.
2012-05-16 | GSE30334 | GEO
Project description:Muscle development and growth is an economically important process in the pig.The neonatal period is another important stage for the pig when the most rapid gain occurring in skeletal muscle.Gene expresseion changes during fetal and postnatal skeletal muscle development that can be used to enhance pig production efficiency, as well as for comparative developmental biology using the pig as a model for other mammalian species. We used microarrays to detail the global programme of gene expression level at different stages of postnatal development. Pig skeletal muscles were selected at different stages of post-natal development for RNA extraction and hybridization on Affymetrix microarrays.So,we sampled at four time-points: within 24 hours after birth (0d),7 days after birth (7d), 14 days after birth (14d), 21 days after birth (21d).
2010-07-07 | E-GEOD-22487 | biostudies-arrayexpress
Project description:To obtain an overview of the transcriptome landscape in developing pig skeletal muscle, 81 high-quality transcriptome libraries that covered 27 developmental stages (3 biological replicates per stage) in pig skeletal muscle were produced by strand-specific rRNA-depleted total RNA sequencing (RNA-seq). We generated 8.59 billion paired-end reads (150 bp × 2) covering 1.24 Tb of sequence for RNA-seq.
2020-09-01 | GSE157044 | GEO
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:<p>Skeletal muscles, accounting for 40% of mammalian body mass, exhibit pronounced heterogeneity due to distinct anatomical locations. Animal husbandry excessively focuses on longissimus dorsi (LDM) development, while neglecting other muscles. In this study, we integrated Bulk RNA Sequencing (bulk RNA-seq) and Liquid Chromatography-Mass Spectrometery (LC-MS) analyses of Soleus (SOL), Gastrocnemius (GAS), and Psoas major (PMM) across three key stages in Duroc pigs. As a result, we identified 9 critical genes (S100A1, MBOAT2, CA3, GYG2, ACTN3, ENO3, SLC3A2, SLC16A10, and GAPDH) and 8 metabolites potentially involved in regulating both skeletal muscle development and fiber-type transformation. The heterogeneity between SOL and GAS was low at birth but increased gradually during development. In contrast, PMM exhibited high heterogeneity compared to SOL and GAS from birth. Notably, expression levels of MYH7, MYH1, and MYH4 displayed stage-specific and muscle type-dependent variations. Moreover, we observed a developmental shift from the MAPK signaling pathway (1-21 d) to the regulation of actin cytoskeleton (21-120 d). Pairwise comparisons between SOL, GAS, and PMM revealed signaling pathways enriched in muscle fiber-type switching. Collectively, through the integration of bulk RNA-seq and LC-MS data, this study provides novel molecular breeding strategies for genetic improvement in meat-producing animals.</p>
2025-09-09 | MTBLS12963 | MetaboLights
Project description:During the maturation of myofibers, the expression and activity of the basic leucine zipper TF Maf are increased compared to developmental stages. To determine the gene program regulated by this TF, we performed ChIP-seq against Maf and H3K27ac in adult gastrocnemius and quadriceps skeletal muscles.
2023-05-31 | GSE211541 | GEO
Project description:Amyotrophic lateral sclerosis (ALS) is a lethal motor neuron disease that progressively debilitates neuronal cells that control voluntary muscle activity. In a mouse model of ALS that expresses mutated human superoxide dismutase 1 (SOD1-G93A) skeletal muscle is one of the tissues affected early by mutant SOD1 toxicity. Fast-twitch and slow-twitch muscles are differentially affected in ALS patients and in the SOD1-G93A model, fast-twitch muscles being more vulnerable. We used miRNA microarrays to investigate miRNA alterations in fast-twitch (EDL) and slow-twitch (soleus) skeletal muscles of symptomatic SOD1-G93A animals and their age-matched wild type littermates.
2014-03-04 | GSE55507 | GEO
Project description:Transcriptional profiling between two different skeletal muscles (Longissimus and Semimembranosus) in pig
2013-01-10 | GSE33957 | GEO