|
| Status |
Public on Sep 17, 2011 |
| Title |
VPA, 4 hrs, ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
ES cells, VPA, 4hrs, H3K9ac ChIP
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14
cell type: embryonic stem cells (ESCs)
treatment: valproic acid (VPA)
time: 4 hours
chip antibody: anti-H3K9ac
antibody vendor: Millipore/Upstate
antibody catalog #: 06942
antibody lot#: 31636
|
| Treatment protocol |
0.5mM VPA was added to the cell medium in the indicated samples for either 4 or 16 hrs.
|
| Growth protocol |
Cells were grown on mitomycin-C-treated primary embryonic fibroblasts, with ES cell medium with 15% FBS and leukemia inhibitory factor.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was cross-linked with 1% formaldehyde (10 min, 37°C), incubated with glycine (125 mM, 10 min, room temp.), and washed with cold PBS. Cells were harvested and sonicated to generate DNA fragments of 100 to 500 bp. Chromatin was immunoprecipitated with 1 μg of H3K9ac-specific antibody. Cross-linking was reversed by incubation for 4 hrs at 65°C under high-salt conditions. The DNA was extracted with phenol-chloroform, precipitated with ethanol, and dissolved in TE. Preparation of sequence libraries and SOLiD sequencing were performed according to the manufacturer’s instructions and kits (Applied Biosystems) at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
VPA 4 hr
|
| Data processing |
Sequence reads were mapped to the mouse mm9 (July, 2007) genome sequence using Bowtie 0.12.5, allowing up to 2 mismatches. Only uniquely mapped reads were reported.
|
| |
|
| Submission date |
Sep 17, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Eran Meshorer |
| E-mail(s) |
meshorer@cc.huji.ac.il
|
| Phone |
+972-2-6585161
|
| Fax |
+972-2-6586073
|
| URL |
http://meshorerlab.huji.ac.il/
|
| Organization name |
The Hebrew University of Jerusalem
|
| Department |
Genetics
|
| Lab |
Stem cell chromatin
|
| Street address |
Edmond J. Safra campus
|
| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
| |
|
| Platform ID |
GPL9318 |
| Series (2) |
| GSE23958 |
Gene expression and H3K9ac genome-wide maps following HDAC inhibition in mouse ES cells |
| GSE24211 |
Genome-wide H3K9 acetylation state before and after VPA treatment |
|
| Relations |
| SRA |
SRX037103 |
| BioSample |
SAMN00189395 |
| Named Annotation |
GSM595516_H3K9Ac_4hr_alignment.bed.gz |
