|
Status |
Public on Feb 27, 2014 |
Title |
Zic3 8hrs embryo |
Sample type |
SRA |
|
|
Source name |
8hpf embryos
|
Organism |
Danio rerio |
Characteristics |
developmental stage: 8hpf embryos tissue: Whole embryo genetic background: AB strain genotype: wild type 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 8hrs 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: CZE017-8hrs-embryo-zic3-peaks.txt: zv9 CZE017-zv9-zic3-6cols.tags: 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 |
SRX193347 |
BioSample |
SAMN01760742 |