|
Status |
Public on May 08, 2012 |
Title |
H3K27ac_48hpf, danRer6 |
Sample type |
SRA |
|
|
Source name |
H3K27ac_48hpf, danRer6
|
Organism |
Danio rerio |
Characteristics |
tissue: whole embryo developmental stage: 48hpf antibody: H3K27ac antibody: Abcam antibody catalog: ab4729 antibody batch: GR6802
|
Growth protocol |
Danio rerio embryos used for ChIP assays were obtained from a natural mating procedure and dechorionated by pronase treatment prior to immunoprecipitation.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
The DNA ends were repaired and the 3-dA overhangs added. The adapters were then ligated. The library was size-selected (200-300 bp) and amplified by PCR.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
|
|
Description |
chromatin IP against H3K27ac
|
Data processing |
Reads were mapped to the D. rerio genome (ENSEMBL version Zv8) with the ELAND software (Ilumina pipeline). Only the alignments within 2 mismatches were included in further analysis. Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
|
|
|
Submission date |
Sep 29, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Ozren Bogdanovic |
E-mail(s) |
o.bogdanovic@gmail.com
|
Organization name |
Garvan Institute of Medical Research
|
Department |
Genomics and Epigenetics
|
Street address |
384 Victoria Street
|
City |
Darlinghurst |
State/province |
NSW |
ZIP/Postal code |
2010 |
Country |
Australia |
|
|
Platform ID |
GPL10164 |
Series (1) |
GSE32483 |
Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis |
|
Relations |
Reanalyzed by |
GSM915200 |
SRA |
SRX100792 |
BioSample |
SAMN00738650 |