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Sample GSM2339807 Query DataSets for GSM2339807
Status Public on Feb 22, 2017
Title C3-24
Sample type SRA
 
Source name Control, Timepoint 240
Organism Mus musculus
Characteristics cell line: C2C12
treatment: Control
time: 240 min
replicate: 3
Treatment protocol A six-well plate, containing differentiated C2C12 myotubes was connected to C-dish electrode (IonOptix, Milton, MA, USA). The electrical current was discharged from the carbon electrode immersed in 8 ml differentiation medium added 24 hours before the EPS. Then, EPS was applied by C-pace cell culture stimulator (C-pace EP, IonOptix, Milton, MA, USA)
Growth protocol Mouse skeletal muscle cell line C2C12 (ATCC® CRL­1772™) were seeded into 6-well plates at a density of 1x105 cells/well, cultured in growth medium containing Dulbecco's Modified Eagle's Medium (DMEM; 25 mM glucose) supplemented with 10% fetal bovine serum, and 1% penicillin-streptomycin at 37oC, 5% CO2. After reaching ~90% confluence, differentiation was induced by switching to 2% horse serum. Differentiation medium was changed every day until fully differentiated myotubes was visualized under a light microscope.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated with AllPrep DNA/RNA/miRNA universal kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s instructions.
Genomic DNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo Research Corp, CA, USA) according to the manufacturer’s instructions. Bisulfite primers were designed to span the promoter region of Ppard, Ccnd1, and Nr4a3 genes within -3000 to +2000 base pairs relative to transcriptional start site (TSS) (Table 1, Figure 3) using MethPrimer program (Li and Dahiya, 2002)
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina MiSeq
 
Data processing Reads were trimmed for adapters and low quality flanking ends using Trim Galore v0.3.7 and Cutadapt v1.4.2
Pre-processed reads were mapped to the mouse reference genome (mm10) with Bismark
Gene coverages were computed with featureCounts and the Gencode v19 annotation
Differential methylation was tested with analyses of variance and t-tests
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file with differential DNA methylation statistics of EPS versus Control, tab delmited text file with DNA methylation levels of targeted genes (genes along rows, samples along columns)
 
Submission date Oct 07, 2016
Last update date May 15, 2019
Contact name Lars Roed Ingerslev
E-mail(s) ingerslev@sund.ku.dk
Organization name Copenhagen University
Department NNF Center for Basic Metabolic Research
Lab Integrative Physiology
Street address Blegdamsvej 3B
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL16417
Series (2)
GSE87747 An electrical pulse stimulation protocol to study acute epigenetic response to muscle cell contraction uncovers acute hydroxymethylation of the exercise-responsive gene Nr4a3 [Bisulfite-Seq]
GSE87749 An electrical pulse stimulation protocol to study acute epigenetic response to muscle cell contraction uncovers acute hydroxymethylation of the exercise-responsive gene Nr4a3
Relations
BioSample SAMN05879224
SRA SRX2229331

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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