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Sample GSM4478809 Query DataSets for GSM4478809
Status Public on Feb 26, 2022
Title ATAC-seq in amphioxus, control sample, replicate 4
Sample type SRA
 
Source name ATAC-seq in amphioxus, control sample
Organism Branchiostoma lanceolatum
Characteristics developmental stage: 15h
treatment: control sample
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_Control_rep4
Amphi_ATAC_Control_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 SAMN14605432
SRA SRX8123881

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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