|
| Status |
Public on Feb 26, 2022 |
| Title |
ATAC-seq in amphioxus, Wnt treatment, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
ATAC-seq in amphioxus, Wnt treatment
|
| Organism |
Branchiostoma lanceolatum |
| Characteristics |
developmental stage: 15h
treatment: Wnt treatment
tissue: whole embryo
|
| Growth protocol |
Embryos were cultivated at 19°C in filtered seawater until desired developmental stage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were centrifugated at 13000 rpm for 1 min, and then seawater wasa carefully removed. Cells were lysed by gently pipetting in cold lysis buffer
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 |
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Wnt_rep2
Amphi_ATAC_Wnt_IDR_peaks.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 Bl71 (Marlètaz et al., 2018. Nature 564:64-70. doi: 10.1038/s41586-018-0734-6), Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: BED files with peaks called using Irreproducibility Discovery Rate (IDR) framework
|
| |
|
| Submission date |
Apr 16, 2020 |
| Last update date |
Feb 26, 2022 |
| 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 |
GPL24210 |
| Series (2) |
| GSE148781 |
Gain of gene regulatory network interconnectivity at the origin of vertebrates [ATAC-seq] |
| GSE148783 |
Gain of gene regulatory network interconnectivity at the origin of vertebrates |
|
| Relations |
| BioSample |
SAMN14605456 |
| SRA |
SRX8123891 |
