NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE136754 Query DataSets for GSE136754
Status Public on Dec 05, 2019
Title Epigenetic and transcriptomic characterization of pure adipocyte fractions from obese pigs identifies candidate pathways controlling metabolism
Organism Sus scrofa
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Reprogramming of adipocyte function in obesity is implicated in metabolic disorders like type 2 diabetes. Here, we used the pig, an animal model sharing many physiological and pathophysiological similarities with humans, to perform in depth epigenomic and transcriptomic characterization of pure adipocyte fractions. Using a combined DNA methylation capture sequencing and Reduced Representation bisulfite sequencing (RRBS) strategy, we identified 2479 differentially methylated regions (DMRs) located at close proximity to-, or within genes. By sequencing of the transcriptome from the same adipocyte cells, we identified 276 differentially expressed transcripts with at least one or more DMRs. These transcripts were over-represented in gene pathways related to MAPK, insulin and adipocytokine signaling. Using a candidate gene approach, we further characterized 13 genes potentially regulated by DNA methylation and identified putative transcription factor binding sites that could be affected by the differential methylation in obesity. Our data constitute a valuable resource for further investigations aiming to delineate the epigenetic etiology of metabolic disorders.
 
Overall design MeDip-seq, RRBS-seq and RNA-seq of adipocytes from lean and obese pigs.
 
Contributor(s) Jacobsen MJ, Havgaard JH, Anthon C, Junker Mentzel CM, Cirera S, Sørensen PM, Pundhir S, Karlskov-Mortensen P, Bruun CS, Lesnik P, Guerin M, Gorodkin J, Jørgensen CB, Fredholm M, Barrès R
Citation(s) 31921306
Submission date Sep 03, 2019
Last update date Feb 26, 2020
Contact name Christian Anthon
E-mail(s) anthon@rth.dk
Phone +4521510929
Organization name University of Copenhagen
Department Veterinary and Animal Sciences
Lab RTH
Street address Thorvaldsens Vej 57
City Frederiksberg C
ZIP/Postal code 1871
Country Denmark
 
Platforms (1)
GPL11429 Illumina HiSeq 2000 (Sus scrofa)
Samples (57)
GSM4057261 totalRNA-seq from pig-402
GSM4057262 totalRNA-seq from pig-407
GSM4057263 totalRNA-seq from pig-413
Relations
BioProject PRJNA563583
SRA SRP220117

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136754_RAW.tar 7.7 Mb (http)(custom) TAR (of TSV)
GSE136754_dataset_all.gt.Obese_Lean.diffReps.hotspot.tsv.gz 35.0 Kb (ftp)(http) TSV
GSE136754_dataset_all.gt.Obese_Lean.diffReps.tsv.gz 743.8 Kb (ftp)(http) TSV
GSE136754_gene_exp.diff.tsv.gz 808.3 Kb (ftp)(http) TSV
GSE136754_metilene.5.Obese_Lean.3-3.out.tsv.gz 62.3 Kb (ftp)(http) TSV
GSE136754_metilene.5.Obese_Lean.5-5.out.tsv.gz 16.0 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap