|
| Status |
Public on Dec 18, 2020 |
| Title |
DMZ_Rep2_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 |
SAMN14145497 |
| SRA |
SRX7759344 |
