|
| Status |
Public on Jul 31, 2015 |
| Title |
MDChB |
| Sample type |
SRA |
| |
|
| Source name |
ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MyoD
|
| Organism |
Mus musculus |
| Characteristics |
cell line: P19
transduction: MyoD
chip antibody: MyoD antibody 6975
|
| Treatment protocol |
P19 cells were infected in MEMα media containing polybrene at a final concentration of 8 µg /ml. After 24 hours, media was replaced with fresh MEMα, and after 48 hours, cells were transitioned to Neurobasal media (GIBCO) containing B27 supplement and 5 mm glutamine(8). Neurobasal media was replaced every 24 hours until cells were harvested.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% formaldehyde for 11 minutes, quenched with glycine, lysed, and then sonicated to generate final DNA fragments of ~150-600 bp.
The soluble chromatin was diluted 1:10 and pre-cleared with a 1:1 Protein A:G slurry for 2 hours at 4oC. Chromatin was mixed with antibody overnight at 4oC, then Protein A:G beads for 2 hours. Beads were washed and de-crosslinked overnight for ~16 hours in 1% SDS, 0.1M NaHCO3 and 70 ug Proteinase K. The MyoD and NeuroD2 antibodies were raised in our lab.
Sequencing libraries were constructed using Nugen Ovation Ultralow Multiplex DR.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
P19MD
Processed data file: MD.bed.gz
|
| Data processing |
Basecalls were performed using CASAVA version 1.8.2.
Reads were aligned to the mm9 genome using BWA (0.7.5).
Peaks were called using in-house peak calling algorithm.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: ChIP-Seq peaks in bed format.
|
| |
|
| Submission date |
Jan 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Tapscott |
| E-mail(s) |
stapscot@fredhutch.org
|
| Organization name |
Fred Hutch Cancer Research Center
|
| Department |
Human Biology
|
| Lab |
Tapscott
|
| Street address |
1100 Fairview N. Ave
|
| City |
Seattle |
| State/province |
WASHINGTON |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE64626 |
Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage [ChIP-seq] |
| GSE64627 |
Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage |
|
| Relations |
| BioSample |
SAMN03280706 |
| SRA |
SRX837355 |
