|
| Status |
Public on Feb 24, 2014 |
| Title |
4C-Seq for Irx3a promoter in 24hpf zebrafish |
| Sample type |
SRA |
| |
|
| Source name |
24hpf zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryos
promoter: Irx3
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated manually before fixation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Mapping: reads were mapped to the Mus musculus (mm9 assembly) or Danio rerio (danRer6 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
|
| |
|
| Submission date |
Nov 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan J. Tena |
| E-mail(s) |
jjtenagu@upo.es
|
| Organization name |
CABD/CSIC
|
| Street address |
Univ. Pablo Olavide, Ctra. Utrera km1
|
| City |
Sevilla |
| ZIP/Postal code |
41013 |
| Country |
Spain |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE52830 |
Obesity-associated variants within FTO form long-range functional connections with IRX3 |
|
| Relations |
| BioSample |
SAMN02427410 |
| SRA |
SRX385389 |
