 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 22, 2017 |
| Title |
E2-3 |
| Sample type |
SRA |
| |
|
| Source name |
EPS, Timepoint 30
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
treatment: EPS
time: 30 min
replicate: 2
|
| 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) |
[email protected]
|
| 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 |
SAMN05879206 |
| SRA |
SRX2229344 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
