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Sample GSM4322293 Query DataSets for GSM4322293
Status Public on Dec 18, 2020
Title DMZ_Rep1_ATAC-Seq
Sample type SRA
 
Source name Tissue
Organism Xenopus tropicalis
Characteristics cell line: none
Stage: stage10 .5 (Gastrula)
antibody: none
Extracted molecule genomic DNA
Extraction protocol ATAC-seq was performed as described (Bright & Veenstra, 2018). Library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit for checking the fragment size distribution and signal to noise ratio was checked by performing qPCR primers spanning open and closed regions.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing After demultiplexing, the reads were aligned to the X. tropicalis genome (xt9) with bowtie2 (Langmead & Salzberg, 2012) using default settings.
All mapped reads were offset by +4 bp for the +strand and −5 bp for the −strand. Peaks were called for each sample using MACS2 (Zhang et al., 2008) with parameters “-q 0.05 --nomodel --shift 37 --extsize 73".
Genome_build: xt9
 
Submission date Feb 20, 2020
Last update date Dec 18, 2020
Contact name Ann Rose Bright
Organization name RIMLS
Department Department of Molecular Biology
Street address Geert Grooteplein Zuid 30
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
 
Platform ID GPL24884
Series (1)
GSE145619 Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates
Relations
BioSample SAMN14145499
SRA SRX7759343

Supplementary file Size Download File type/resource
GSM4322293_ATACseq_Blastoporelip_R1_peaks.bed.gz 320.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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