|
| Status |
Public on Feb 11, 2009 |
| Title |
Midbrain_p300_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic day 11.5 (e11.5) midbrain
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1 Gender: Mixed male / female Age: embryonic day 11.5 (e11.5) Tissue: midbrain
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic forebrain, midbrain and limb tissue was isolated from CD-1 mouse embryos at e11.5. Tissue samples were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation using an anti-p300 antibody. ChIP DNA was sheared by sonication, end-repaired, ligated to solexa sequencing adapters and amplified by emulsion PCR. Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the Solexa / Illumina Genome Analyzer to generate 36 bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Tissue pooled from ~150 embryos Chromatin IP against p300
|
| Data processing |
Sequence reads were aligned to the mouse reference genome (mm9) using BLAT. Uniquely aligned reads were extended to 300bp in the 3' direction and used to determine the read coverage at individual nucleotides at 25bp intervals throughout the mouse genome. p300-enriched regions (peaks) with an estimated false discovery rate of 0.01, were identified by comparison with a random distribution of the same number of reads. Candidate peaks mapping to repetitive regions were removed as likely artifacts.
|
| |
|
| Submission date |
Dec 05, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew James Blow |
| E-mail(s) |
mjblow@lbl.gov
|
| Phone |
510-486-6590
|
| Fax |
510-486-7004
|
| Organization name |
Lawrence Berkeley National Laboratory
|
| Department |
Genomics Division
|
| Lab |
Rubin / Pennacchio
|
| Street address |
1 Cyclotron Road
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE13845 |
ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers |
|
| Relations |
| SRA |
SRX002662 |
| BioSample |
SAMN02195641 |
