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Identification of differentially expressed genes in fetal and postnatal pig skeletal muscle

ABSTRACT: Fetal myogenesis and postnatal skeletal muscle hypertrophy in growing pigs are critical yet poorly understood processes. Global gene expression analyses will increase understanding of these processes by identifying key genes and pathways controlling skeletal muscle development. For this study, a pig 70-mer oligonucleotide microarray was used to identify differentially expressed genes in hind limb skeletal muscle of pigs at 60 days of gestation and 7 weeks of age. This oligonucleotide microarray experiment revealed 162 genes that were differentially expressed between 60 day fetal and 7 week postnatal samples. Relative real-time RT-PCR was used to confirm differential expression of three genes. This experiment identified genes exhibiting different developmental patterns of gene expression in pig skeletal muscle. Keywords: developmental study

ORGANISM(S): Sus scrofa

PROVIDER: GSE4958 | GEO | 2006/09/01

SECONDARY ACCESSION(S): PRJNA96709

REPOSITORIES: GEO

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Identification of differentially expressed genes in fetal and postnatal pig skeletal muscle

Project description:Fetal myogenesis and postnatal skeletal muscle hypertrophy in growing pigs are critical yet poorly understood processes. Global gene expression analyses will increase understanding of these processes by identifying key genes and pathways controlling skeletal muscle development. For this study, a pig 70-mer oligonucleotide microarray was used to identify differentially expressed genes in hind limb skeletal muscle of pigs at 60 days of gestation and 7 weeks of age. This oligonucleotide microarray experiment revealed 162 genes that were differentially expressed between 60 day fetal and 7 week postnatal samples. Relative real-time RT-PCR was used to confirm differential expression of three genes. This experiment identified genes exhibiting different developmental patterns of gene expression in pig skeletal muscle. Oligonucleotide microarrays used for this study consisted of 13,297 70-mer oligos (Pig Array-Ready Oligo Set v. 1.0 and Pig Oligo Extension Set v. 1.0, Qiagen, Inc., Valencia, CA) each spotted once on a single slide . Controls included 76 Arabidopsis thaliana gene spots, 17 beta tubulin spots, 17 glyceraldehyde-3-phosphate dehydrogenase spots, 85 heat shock protein gene spots, 69 ribosomal protein gene spots, 112 randomly generated negative control spots and 470 blanks. The oligonucleotide microarray was screened with samples obtained from pigs at 60 days of gestation and 7 weeks of age postnatal (n = 3 per age). Six oligonucleotide microarray slides were screened. All samples were used twice, labeled once with Cy3 and once with Cy5, and each 60 day gestation sample was randomly paired with two different 7 week postnatal samples.

2010-07-01 | E-GEOD-4958 | biostudies-arrayexpress

Expression data from neonatal pig skeletal muscle

2010-06-22 | GSE22487 | GEO

Expression data from neonatal pig skeletal muscle

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

Sus scrofa

Project description:Identification of differentially expressed genes in fetal and postnatal pig skeletal muscle

| PRJNA96709 | ENA

Expression data from longissimus dorsi muscle of Shaziling pig at 25-days old and longissimus dorsi musle of Yorkshire pig at 25-days old

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

Deletion of DMD exon 52 in the pig results in fulminant muscular dystrophy

Project description:Duchenne muscular dystrophy (DMD) is caused by mutations in the X-linked dystrophin (DMD) gene. The absence of dystrophin protein leads to progressive muscle weakness and wasting, disability and death. To establish a tailored large animal model of DMD, we deleted DMD exon 52 in male pig cells by gene targeting and generated offspring by nuclear transfer. DMD pigs exhibit absence of dystrophin in skeletal muscles, increased serum creatine kinase levels, progressive dystrophic changes of skeletal muscles, impaired mobility, muscle weakness, and a maximum life span of 3 months due to respiratory impairment. To address the accelerated development of muscular dystrophy in DMD pigs as compared to human patients, we performed a genome-wide transcriptome study of M. biceps femoris samples from 2-day-old and 3-month-old DMD and age-matched wild-type pigs. The transcriptome changes in 3-month-old DMD pigs were in good accordance with the findings of gene expression profiles in human DMD, reflecting the processes of degeneration, regeneration, inflammation, fibrosis, and impaired metabolic activity. The transcriptome profile of 2-day-old DMD pigs pointed towards increased protein and DNA catabolism, reduced extracellular matrix formation and cell proliferation and showed similarities with transcriptome changes induced by exercise injury in muscle. Our transcriptome studies provide new insights into congenital changes associated with dystrophin deficiency and secondary complications arising during postnatal development. Thus the DMD pig is a useful model to determine the hierarchy of physiological derangements in dystrophin-deficient muscle. 13 samples, two conditions, two age-groups, 3-4 biological replicates

2013-08-06 | E-GEOD-44096 | biostudies-arrayexpress

Comparative transcriptome analysis reveals genes regulating myogenesis and adipogenesis in Laiwu pigs over four developmental stages

Project description:We performed transcriptome analysis of the longissimus dorsi (LD) muscle during four development stages (60, 120, 240 and 400 days after birth) in Laiwu pigs, an indigenous fatty pig breed in North China. This study provides a reference for exploring transcriptome regulation mechanisms affecting muscle growth and development in obese pigs.

2016-11-23 | GSE90135 | GEO

LongSAGE analysis in skeletal muscle at three prenatal stages in lean and obese pig breeds

Project description:Obese and lean pig breeds showed obvious phenotypic variations and physiological differences in skeletal muscle growth. Prenatal muscle development programs postnatal performance. In this study we initially conducted full transcriptional profiling of prenatal skeletal muscle from Tongcheng pigs (obese) and Landrace pigs (lean) at 33, 65 and 90 days post coitus (dpc), using long serial analysis of gene expression (LongSAGE). We subsequently sequenced 317,115 LongSAGE tags and identified 1400 and 1201 differentially expressed transcripts that showed eight expression patterns for Tongcheng and Landrace, respectively. These two breeds had more significant differences in their gene expression profiles at 65 than that at 33 and 90 dpc. We also identified 532, 653 and 459 transcripts that were differentially expressed at 33, 65 and 90 dpc between the two breeds, respectively. The cellular function of the differentially expressed transcripts that matched annotated genes revealed that each stage had a uniquely altered profile between the two breeds in various functional categories including muscle fiber constitute and contraction, apoptosis, protein synthesis, and signalling transduction. Our results suggest that skeletal muscle development potentially has a greater lag in its growth rate at 33-65 dpc in Tongcheng pigs when compared with their Landrace counterparts. Our analyses therefore not only will provide valuable resources in the further identification of candidate genes for meat production traits, but also assist in the elucidation of the development of prenatal skeletal muscle in pigs and other vertebrates. Keywords: comparative transcriptome analysis

2007-08-10 | GSE5494 | GEO

Effect of Dietary Lysine on the Gene Expression Profile of Skeletal Muscle in Finishing Pigs

Project description:The main goal of swine production is to convert feedstuffs into edible meat whose major component is skeletal muscle. The overall objective of this project is to study the effect of dietary lysine on the gene expression profile of skeletal muscle in late stage finishing pigs. The hypothesis for this is that adequate or excess level of dietary lysine will change the expression levels of numerous genes, and these changes are in favor of muscle protein accretion and are associated with various blood metabolites and growth performance parameters. Three experimental (lysine-deficient, lysine-adequate, lysine-excess) diets were respectively fed to 3 groups of pigs (initial body weight, ~95 kg/pig; 3 pigs/group) for a total of 5 weeks.

2016-02-09 | E-GEOD-77708 | biostudies-arrayexpress

Deletion of DMD exon 52 in the pig results in fulminant muscular dystrophy

2013-08-06 | GSE44096 | GEO

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