|
| Status |
Public on Feb 27, 2014 |
| Title |
Zic3 24hrs sorted |
| Sample type |
SRA |
| |
|
| Source name |
24hpf embryos
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 24hpf embryos
cell type: FACS sorted zic3 expressing cell from 24hpf embryo
genetic background: AB strain
genotype: sqet33 transgenic
chip antibody: Zic3
|
| Growth protocol |
Zebrafish of wild type (AB strain) and transgenic line SqET33 (Kondrychyn et al., 2009; Parinov et al., 2004) were maintained according to established protocols (Westerfield, 1993). Embryos were staged according to standard morphological criteria (Kimmel et al. 1995).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin Immunoprecipitation (ChIP) was performed according to a published protocol (Wardle et al., 2006) with an addition of a deyolking step according to Link and colleagues (2006), with modifications.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Zic3 ChIP-seq of sorted cells from 24hr embryo
|
| Data processing |
Sequencing reads were mapped to the zebrafish genome assembly version July 2010 (Zv9), following which peak finding was performed using the QuEST algorithm (Valouev et al., 2008)
Genome Build:
CZE019-24hrs-sorted-zic3-peaks.txt: zv9
CZE019.bed: zv9
|
| |
|
| Submission date |
Oct 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Vibhor Kumar |
| E-mail(s) |
kumarv1@gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Department |
CMB-6
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL10164 |
| Series (1) |
| GSE41458 |
Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes |
|
| Relations |
| SRA |
SRX193349 |
| BioSample |
SAMN01760744 |
