Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation profiles (RRBS) of the muscle of pigs distinct in metabolic types and genetic background

ABSTRACT: DNA methylation is an epigenetic mechanism that plays roles in gene regulation and expression. This study aims to profile DNA methylation at genome-wide scale and single base resolution using reduced representation bisulfite sequencing (RRBS) of the muscle of pigs differing in muscle metabolism and genetic background. Pietrain homozygous- positive (PiPP) and negative (PiNN) for the ryanodine receptor mutation and malignant hyperthermia-susceptible (MHS), Duroc and F2 crossbred Duroc-Pietrain homozygous-negative (DuPi) pigs were investigated to identify differentially methylated CpG sites/ regions and to integrate the results with gene expression data.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Sus scrofa

SUBMITTER: Nares Trakooljul

PROVIDER: E-MTAB-7338 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression studies to identify skeletal muscle genes related to stress in pigs

Project description:Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by pre-slaughter stress or no stress treatment in pigs of different breed (Italian Duroc, Italian Large White or Pietrain) and differnt Halothane genotype (RYR1 locus CC-NN, CT-Nn or TT-nn) in Pietrain pigs.

2013-01-01 | GSE13115 | GEO

Gene expression studies to identify skeletal muscle genes related to stress in pigs

2013-01-01 | E-GEOD-13115 | biostudies-arrayexpress

Identification of global copy number variations among diverse pig breeds by a CGH array

Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0). In this study, a custom-made tiling oligo-nucleotide 720k array was used with a median probe spacing of 2506 bp for screening 12 pigs with a female Duroc as the reference. WD: White Duroc (♀); YX: Yangxin (♂); EH: Erhualian (♀); TC: Tongcheng (♀); LW: Large White (♀); PT: Pietrain (♂); LD1: Landrace × DIV pig 1 (♂); LD2: Landrace × DIV pig 2 (♀); DIV1: Chinese new pig line DIV 1 (♀); DIV2: Chinese new pig line DIV 2 (♀); L1: Landrace 1 (♂); L2: Landrace 2 (♂).

2013-08-09 | E-GEOD-41488 | biostudies-arrayexpress

Gene expression in Longissimus lumborum and Semimembranosus skeletal muscles in pig using the GenmascqChip (custom 15K Agilent microarray)

Project description:Transcriptional profiling between two different skeletal muscles (Longissimus and Semimembranosus) in pig The 90 pigs (females and barrows) used in gene expression analyses are part of a larger F2 population of 1,000 animals, setup within the framework of a QTL detection program. These animals were produced as a second generation intercross between two commercial sire lines (F016, Pietrain type line, and FH019, synthetic line from Hampshire, Duroc and Large-White founders, FRANCE-HYBRIDES, St Jean de Braye, France).

2013-01-10 | E-GEOD-33957 | biostudies-arrayexpress

Gene expression in Longissimus lumborum in pig using the GenmascqChip (custom 15K Agilent microarray)

Project description:Genetic variability of transcript abundance in pig skeletal muscle at slaughtering. The 325 pigs (females and barrows) used in gene expression analyses are part of a larger F2 population of 1,000 animals, setup within the framework of a QTL detection program. These animals were produced as a second generation intercross between two commercial sire lines (F016, Pietrain type line, and FH019, synthetic line from Hampshire, Duroc and Large-White founders, FRANCE-HYBRIDES, St Jean de Braye, France).

2012-04-04 | E-GEOD-28714 | biostudies-arrayexpress

DNA methylation profiling of the amygdala, hippocampus, hypothalamus and adrenal gland of the pig using Reduced Representation Bisulfite Sequencing (RRBS)

Project description:Three brain regions of the limbic system, the amygdala, hippocampus and hypothalamus, are responsible for survival behaviors such as feeding and physical challenging. Hypothalamus works together with pituitary and adrenal gland (HPA-axis) to adjust homeostatic state by modulating stress-response hormones. Unraveling molecular signatures such as DNA methylation of these tissues may provide deeper insights into a link between epigenetic regulation and phenotypic plasticity of behavioral responses of animals. We examined the DNA methylation profile of amygdala (n = 20), hippocampus (n = 20), hypothalamus (n = 19) as well as a non-brain tissue, adrenal gland (n=19) of German Landrace pigs using a cost effective method, Reduced Representation Bisulfite Sequencing (RRBS).

2024-11-19 | E-MTAB-10640 | biostudies-arrayexpress

Genome-wide linkage analysis of global gene expression of loin muscle tissue identifies putatively cis-acting candidate genes in pigs

Project description:510 F2 Duroc X Pietrain pigs together with their parents and grandparents from a resource population at Michigan State University were genotyped for 124 microsatellite markers. Transcriptional profiling was performed on a subset of 176 F2 pigs using a 70-mer long oligonucleotide microarray containing 20,400 oligos (GPL7435). Pigs were selected for transcriptional profiling using a selective phenotyping strategy which consisted in choosing the two extreme males and females for a trait of interest within each litter.

2010-08-11 | GSE23351 | GEO

Genome-wide linkage analysis of global gene expression of loin muscle tissue identifies putatively cis-acting candidate genes in pigs

2010-08-11 | E-GEOD-23351 | biostudies-arrayexpress

Gene expression data of mRNA from skeletal muscle sample of pig breed Duroc and Pietrain with malignant hyperthermia syndrome homozygous negative

Project description:47,880 probe-sets were screened, in the first part of this study, they were analysed for differential expression between different breeds (Duroc and Pietrain) at adult stage. RNAs of skeletal muscle from Duroc and Pietrain at adult stage were hybridized to Affymetrix Porcine Snowball Array.

2016-06-01 | E-GEOD-69840 | biostudies-arrayexpress

DNA methylation profiling (RRBS) of differentiating porcine synovial mesenchymal stem cells (PSMSCs) during the course of osteogenic induction

Project description:This study aims to investigate DNA methylation of differentiating synovial mesenchymal stem cells (psMSCs) isolated from German Landrace (DL) and Angeln Saddleback (AS) pigs previously characterized and described (Siengdee et al 2020, Frontiers in Cell and Developmental Biology). The 3rd passage of psMSCs were induced to differentiate in osteogenic differentiation media. DNA methylation profiles by Reduced Representation Bisulfite Sequencing (RRBS) of the differentiating cells were compared with the undifferentiated control cells at day 1, 7, 14 and 21 post-osteogenic induction to identify differentially methylated CpGs during the course of differentiation and between pig breeds (DL vs AS).

2024-12-01 | E-MTAB-9913 | biostudies-arrayexpress

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