|
| Status |
Public on Jan 03, 2011 |
| Title |
HL1_H3ac_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
mouse cardiomyocytes (HL1-cells)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: cardiomyocytes
cell line: HL-1
antibody: H3ac
|
| Growth protocol |
HL-1 cells were provided by Prof. William C. Claycomb and cultured as described (Claycomb et al. (1998) HL1 cells: a cardiac muscle cell line that contracts and retains phenozypic characteristics of the adult cardiomyocytes. Proc Natl Acad Sci USA 95(6):2979-2984.). The cells were harvested for experiments at their maximum concentration.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared for sequencing according to Illumina's library preparation instructions. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H3ac
|
| Data processing |
Image analysis and base calling was done using the open source Firecrest and Bustard applications (Solexa Pipeline 1.4.0). The resulting sequence reads were mapped to the mouse reference genome (NCBI v37, mm9) using the read mapper RazerS. Only unique mapped 36nt reads with at most two mismatches were retained. To identify transcription factor Srf binding sites as well as histone 3 acetylated regions we used the CisGenome software. The final processed peak list contains peak identifier, chromosome number, start and end position.
|
| |
|
| Submission date |
Nov 17, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Silke Sperling |
| E-mail(s) |
silke.sperling@charite.de
|
| 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 |
GPL9185 |
| Series (2) |
| GSE19065 |
Identification of transcription factor Srf binding sites and histone 3 actetylated regions in mouse cardiomyocytes |
| GSE26397 |
The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5 and Srf, Histone Modifications and MicroRNAs |
|
| Relations |
| SRA |
SRX018660 |
| BioSample |
SAMN00010777 |
