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Status |
Public on Feb 26, 2022 |
Title |
ATAC-seq in amphioxus, control sample, replicate 4 |
Sample type |
SRA |
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Source name |
ATAC-seq in amphioxus, control sample
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Organism |
Branchiostoma lanceolatum |
Characteristics |
developmental stage: 15h treatment: control sample tissue: whole embryo
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Growth protocol |
Embryos were cultivated at 19°C in filtered seawater until desired developmental stage
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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
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 4000 |
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Description |
Amphioxus (Branchiostoma lanceolatum) Amphi_ATAC_Control_rep4 Amphi_ATAC_Control_IDR_peaks.bed
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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
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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 |
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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 |
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Relations |
BioSample |
SAMN14605432 |
SRA |
SRX8123881 |