|
| Status |
Public on Apr 06, 2023 |
| Title |
ATAC-Seq_LL-ZT4-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mature leaf
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
cultivar: Minghui 63
protocol: constant light (LL)
time-point: ZT4
tissue: mature leaf
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
0.5 g-1 g of rice mature leaves cross-linked with 1% formaldehyde were used in each experiment.
Isolated rice nuclei were permeabilised with 0.3% Triton X-100 for 10 min on ice and then prepared for in situ chromatin digestion by Tn5 transposase (VAHTS; cat. no. TD501) for 30 min at 37 °C at 300 rpm. Digested chromatin was purified using a MiniElute kit (QIAGEN; cat. no. 28004), followed by PCR amplification and size selection.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: bigWig file by deepTools bamCoverage
|
| |
|
| Submission date |
Apr 06, 2023 |
| Last update date |
Apr 17, 2023 |
| Contact name |
guoting chen |
| E-mail(s) |
chenguoting@webmail.hzau.edu.cn
|
| Phone |
+86 13212791520
|
| Organization name |
National Key Laboratory of Crop Genetic Improvement
|
| Street address |
1 Shizishan Street, Hongshan District
|
| City |
Wuhan |
| ZIP/Postal code |
430000 |
| Country |
China |
| |
|
| Platform ID |
GPL26667 |
| Series (2) |
| GSE213089 |
Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq] |
| GSE213227 |
Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice |
|
| Relations |
| SRA |
SRX19900325 |
| BioSample |
SAMN34105577 |
