|
| Status |
Public on Feb 13, 2013 |
| Title |
C2C12 WCE |
| Sample type |
SRA |
| |
|
| Source name |
myotubes
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: None
antibody vendor and catalog number: None WCE
|
| Growth protocol |
C2C12 myoblasts were grown under typical C2C12 myoblast conditions. Myotube formation was induced for 48 hours in 2% horse serum and 1x selenium, transferrin and insulin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. Half of the cell lysate was used for immunoprecipitation. The chromatin extracts containing DNA fragments with an average size of 500 bp were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
WCE for C2C12 myotubes
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 1 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended by MACS and allocated into 50bp bins
|
| |
|
| Submission date |
Feb 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE44286 |
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes [ChIP-Seq] |
| GSE44288 |
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes |
|
| Relations |
| SRA |
SRX236484 |
| BioSample |
SAMN01920472 |
