|
| Status |
Public on May 08, 2012 |
| Title |
H3K4me1_80%epi, danRer6 |
| Sample type |
SRA |
| |
|
| Source name |
H3K4me1_80%epi, danRer6
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
developmental stage: 80% epiboly
antibody: H3K4me1
antibody vendor: Diagenode
antibody catalog: CS-037-100
antibody batch: A399-001
|
| 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 H3K4me1
|
| 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 |
GSM915194 |
| SRA |
SRX100786 |
| BioSample |
SAMN00738644 |
