|
| Status |
Public on Jun 16, 2020 |
| Title |
stage 38 rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Oryzias latipes |
| Characteristics |
strain/background: offspring of d-rR-Tg(olvas-GFP) and Qurt
tissue: Whole embryo
developmental stage: stage 38
|
| Growth protocol |
Embryos were incubated at 28 ◦C fresh water for all time course and processed for ATAC-seq at the indicated times.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Medaka embryos were grown to the indicated times and chorions were removed by incubating in 1mg/mL Pronase. After removed yorks using deyork buffer, embryo tissues were triturated to homogeneity in 1 mL 1X TrypLE™ Express.
ATAC-Seq libraries were prepared using Omni-ATAC protocol and DNA fragments were recovered using mini-ATAC protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Adapters were removed using Trimmomatic (version 0.36).
Mapping by Bowtie (version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter.
PCR duplicates reads were removed using Picard.
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g 7.34e8’.
Peak reads counts were calculated by multicov function from BEDTools.
Genome_build: medaka ASM223467v1
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage; Scores represent reads counts.
|
| |
|
| Submission date |
Aug 19, 2019 |
| Last update date |
Jun 17, 2020 |
| Contact name |
Yongjie Liu |
| E-mail(s) |
liuyongjie15@mails.ucas.ac.cn
|
| Organization name |
Institute of Genetics and Developmental Biology
|
| Street address |
No. 1 West Beichen Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL25587 |
| Series (1) |
| GSE136027 |
Dynamic Transcriptional and Chromatin Accessibility Landscape of Medaka Embryogenesis |
|
| Relations |
| BioSample |
SAMN12604291 |
| SRA |
SRX6743188 |
