|
Status |
Public on Jun 21, 2012 |
Title |
H3K27me3 24hpf |
Sample type |
SRA |
|
|
Source name |
whole embryo
|
Organism |
Danio rerio |
Characteristics |
developmental stage: 24 hpf tissue: whole embryo chip antibody: H3K27me3 chip antibody manufacturer: Millipore chip antibody catalog #: 07-449 chip antibody lot #: JBC1852356 genetic background: mixed Ab and Tubingen
|
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 H3K27me3
|
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 |
Jan 12, 2012 |
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) |
GSE35050 |
Extensive conservation of ancient microsynteny across metazoans |
|
Relations |
SRA |
SRX115499 |
BioSample |
SAMN00771618 |