|
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 |