|
Status |
Public on Feb 24, 2014 |
Title |
4C-Seq for FTO promoter in 24hpf zebrafish |
Sample type |
SRA |
|
|
Source name |
24hpf zebrafish embryos
|
Organism |
Danio rerio |
Characteristics |
tissue: whole embryos promoter: FTO
|
Treatment protocol |
No treatment
|
Growth protocol |
Embryos were raised at 28ÂșC 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 |
SAMN02427412 |
SRA |
SRX385388 |