|
| Status |
Public on May 18, 2015 |
| Title |
Zebrafish_24hpf (35) |
| Sample type |
SRA |
| |
|
| Source name |
24hpf zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 24hpf
tissue: whole embryos
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated with pronase 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 |
library strategy: 4C-Seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) , Danio rerio (danRer7 assembly) or S.purpuratus (StrPur4 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: mm9/danRer7/StrPur4
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 4Cseq of viewpoint that can be directly uploaded to UCSC for visualization.
|
| |
|
| Submission date |
Mar 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Carlos Gómez |
| E-mail(s) |
cgommar@hotmail.com
|
| Organization name |
Centro Andaluz de Biologia del Desarrollo
|
| Street address |
Crta Utrera km 1
|
| City |
Seville |
| State/province |
Seville |
| ZIP/Postal code |
41013 |
| Country |
Spain |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE66900 |
Evolutionary comparison reveals that diverging CCCTC-binding factor (CTCF) sites are signatures of ancestral topological associating domains borders |
|
| Relations |
| BioSample |
SAMN03418304 |
| SRA |
SRX957427 |
