|
| Status |
Public on May 04, 2024 |
| Title |
Shoot, 30D Input |
| Sample type |
SRA |
| |
|
| Source name |
Shoot
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: Shoot
genotype: transgenic pUbi:OsWRKY11-Myc
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A total of 2 g of seedling shoots from transgenic pUbi:OsWRKY11-Myc plants were harvested and fixed in a crosslinking solution containing 1% (w/v) formaldehyde under vacuum for 30 min on ice. crosslinking was terminated by treating with 0.125 mM glycine under vacuum for 5 min.
ChIP assay was performed using the EpiQuik™ Plant ChIP Kit (Epigentek).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The ChIP library underwent quality assessment based on the following criteria: NRF>0.9, PBC1>0.9, and PBC2>3.
The raw sequencing reads were subjected to quality filtering using Trimmomatic (version 0.36) and aligned to the rice reference genome (rice.uga.edu, version 7.0) using bwa (0.7.12-r1039) with default parameters. The peak analysis was conducted using MACS2 (2.2.7.1) with the parameters "-B -f BAMPE -q 0.05".
Assembly: Oryza sativa genome (rice.uga.edu, version 7.0)
Supplementary files format and content: peak
|
| |
|
| Submission date |
Apr 29, 2024 |
| Last update date |
May 04, 2024 |
| Contact name |
Lirong Zhao |
| E-mail(s) |
lrzhao957@gmail.com
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Xishuangbanna Tropical Botanical Garden
|
| Street address |
No.88 Xuefu Road
|
| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650223 |
| Country |
China |
| |
|
| Platform ID |
GPL23013 |
| Series (1) |
| GSE266082 |
Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations |
|
| Relations |
| BioSample |
SAMN41110958 |
| SRA |
SRX24390737 |
