|
| Status |
Public on Jun 14, 2017 |
| Title |
input_DNA_diff |
| Sample type |
SRA |
| |
|
| Source name |
Differentiated C2C12 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: Differentiated C2C12 cells
chip antibody: none (input)
|
| Growth protocol |
C2C12 myoblasts were cultured at 5% CO2 and 37°C in Dulbecco's modified Eagle's medium (Gibco) supplemented with 1% penicillin/streptomycin (Gibco) and 10% fetal bovine serum (Biochrom). Mononucleate C2C12 myocyte cells were harvested before reaching 70% confluence. To induce differentiation, cells were cultured with Dulbecco's modified Eagle's medium and 2% horse serum (Biochrom) and maintained for 48h, when more than 90% of the cells had fused into myocytes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was done with MAGnify™ Chromatin Immunoprecipitation System (life technologies, Cat#: 49-2024) following the manufacturer’s indication with some modifications. Sonication was performed using Biorupter UCD300 to obtain chromatin fragments of approximately between 100-300bp. The following antibodies were used: anti-H3K4me2 (Abcam ab7766), anti-H3K4me3 (Abcam ab8580) and anti-MyoD (Santa Cruz, sc-760).
Libraries were prepared (with modifications) using NEXTflex™ ChIP-Seq Kit (Bioo Scientific, Cat#: 5143). Sequencing was done with Illumina Hiseq 2000, producing 51bp+7 single reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Replicates were merged for the analysis.
|
| Data processing |
Basecalls performed using CASAVA version 1.8.0
ChIP-seq reads were aligned to the reference genome (mm9) using Bowtie (v0.12.9) with default parameters. Ambiguously mapped reads were discarded.
Replicate BAM files were merged using SAMtools (v0.1.18.0).
MACS (v1.4.2) for peak calling which gives peaks and fitted signals as output (Command used – macs14 -t treat.merged.sam -c control.merged.sam -n output -p 1e-04 –B). For MyoD we used peaks and for histone marks we used fitted signals.
Genome_build: mm9
Supplementary_files_format_and_content: MyoD peaks are provided as bed files. Histone marks and input signals are also provided as bed files.
|
| |
|
| Submission date |
Nov 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Silke Sperling |
| E-mail(s) |
[email protected]
|
| Phone |
++49 (0)30 450540123
|
| Organization name |
Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine
|
| Department |
Cardiovascular Genetics
|
| Lab |
Cardiovascular Genetics
|
| Street address |
Lindenberger Weg 80
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE63716 |
Epigenetic analysis reveals the repressive function of MyoD during myogenic differentiation |
|
| Relations |
| BioSample |
SAMN03225498 |
| SRA |
SRX770039 |
