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Sample GSM2333844 Query DataSets for GSM2333844
Status Public on Dec 15, 2016
Title HFD-chow, rep3 (RNA-Seq)
Sample type SRA
Source name HFD-chow, liver
Organism Mus musculus
Characteristics strain: C57BL/6J
treatment: HFD-chow
age: 24 weeks
Treatment protocol C57BL/6J mice (Jackson Laboratory) were fed either a HFD (D12327, Research Diet, 40% fat by calories) or chow diet (NIH-31, Zeigler Brothers Inc., 8% fat by calories) for seven weeks from 12 weeks of age (groups termed HFD and Chow, respectively). After seven weeks, half of the mice where sacrificed by CO2 narcosis followed by cervical dislocation, livers were dissected and processed for RNA purification, nuclei isolation or frozen in liquid nitrogen for subsequent studies. Blood samples were taken as indicated and processed for metabolic measurements. The other half of the animals continued on a chow diet (termed HFD-chow and Chow-chow) for an additional five weeks
Extracted molecule total RNA
Extraction protocol 5 mg of liver tissue were homogenized using UltraThorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) according to manufacturer’s instructions. Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
Purified RNA was subjected to either polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq and libraries of H3K27ac-enriched DNA and DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description SM1970
Data processing Aligment to mm9 using STAR
Differential gene expression and H3K27ac binding identified using DESeq2.
Gene ontology analysis using PANTHER.
To quantify exon and intron RNA reads the iRNA pipeline was used (Madsen, J. G. et al. iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. Nucleic acids research, doi:10.1093/nar/gku1365 (2015).
Pathway analysis of intron-regulated genes using the curated reactome database (Croft, D. et al. The Reactome pathway knowledgebase. Nucleic acids research 42, D472-477, doi:10.1093/nar/gkt1102 (2014).Fabregat, A. et al. The Reactome pathway Knowledgebase. Nucleic acids research 44, D481-487, doi:10.1093/nar/gkv1351 (2016)).
H3K27ac ChIP-seq binding sites identified using HOMER
Enriched motif analysis using DNA motifs for TFs curated by HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
Submission date Oct 03, 2016
Last update date May 15, 2019
Contact name Lars Grøntved
Phone +45 24 60 14 06
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense
ZIP/Postal code 5230
Country Denmark
Platform ID GPL18480
Series (1)
GSE87565 High fat diet-induced changes of mouse hepatic transcription and enhancer activity can be reversed by subsequent weight loss
BioSample SAMN05860360
SRA SRX2208090

Supplementary file Size Download File type/resource
GSM2333844_SM1970_RNA_HFD_chow_rep3.bedgraph.gz 6.8 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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