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Sample GSM8604236 Query DataSets for GSM8604236
Status Public on Nov 30, 2024
Title ATAC-seq in sea star whole embryos at 24 hpf, replicate 2
Sample type SRA
 
Source name whole embryo
Organism Patiria miniata
Characteristics cell type: whole embryo
genotype: WT
time: 24 hpf
Growth protocol Embryos were grown at 15°C in ASW until desired developmental stage
Extracted molecule genomic DNA
Extraction protocol Wild type embryos were 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; Magri MS et al., 2020. Front Cell Dev Biol.24;7:372. doi: 10.3389/fcell.2019.00372; Magri MS et al., 2021. Methods Mol Biol. 2219:253-265. doi: 10.1007/978-1-0716-0974-3_16
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description ATAC-seq
Data processing Alignment: reads were aligned to the 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
Assembly: Patiria miniata 2020 Assembly (Pmin_1.0/GCF_015706575.1)
Supplementary files format and content: narrowPeak files with peaks called using MACS2 with q<0.01
 
Submission date Oct 30, 2024
Last update date Nov 30, 2024
Contact name Marta Silvia Magri
E-mail(s) marta.s.magri@gmail.com
Organization name Centro Andaluz de Biología del Desarrollo
Street address Carretera de Utrera km1
City Seville
ZIP/Postal code 41013
Country Spain
 
Platform ID GPL33874
Series (2)
GSE280529 Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization - ATAC-seq
GSE281904 Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes
Relations
BioSample SAMN44511543
SRA SRX26553607

Supplementary file Size Download File type/resource
GSM8604236_24hpf_wtB.narrowPeak.gz 1.5 Mb (ftp)(http) NARROWPEAK
GSM8604236_pmin1_24hpf_wtB_normalized_nucfree.bw 68.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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