|
| Status |
Public on Aug 15, 2018 |
| Title |
ATACseq zebra dome replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: dome
|
| Growth protocol |
Embryos were cultivated at 28°C in E3 medium until desired developmental stage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Wild type embryos were dechorionated, deyolked and lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ATAC_seq
ATAC_zebra_dome_idrpeaks.bed
|
| Data processing |
Alignment: reads were aligned against reference genome using Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession), Zebrafish September 2014 (GRCz10/danRer10), Medaka October 2005 (oryLat2)
Supplementary_files_format_and_content: BED files with peaks called using Irreproducibility Discovery Rate (IDR) framework
|
| |
|
| Submission date |
Nov 02, 2017 |
| 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 |
GPL21741 |
| Series (2) |
| GSE106428 |
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [ATAC-Seq] |
| GSE106431 |
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits |
|
| Relations |
| BioSample |
SAMN07966237 |
| SRA |
SRX3352467 |
