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Status |
Public on Nov 30, 2024 |
Title |
ATAC-seq in sea star whole embryos at 24 hpf, replicate 2 |
Sample type |
SRA |
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|
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
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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
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|
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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 |