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Status |
Public on May 09, 2023 |
Title |
ZH11_R_H3K18Ace_1_IP |
Sample type |
SRA |
|
|
Source name |
4-leaf stage seedling
|
Organism |
Oryza sativa Japonica Group |
Characteristics |
tissue: 4-leaf stage seedling chip-seq antibody: anti-H3K18Ac (A7257, ABclonal) genotype: ZH11 treatment: Normal
|
Growth protocol |
The rice seeds were sinked in water in the dark for 2-3 days at 37°C, and then 10 days in the hydroculture.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modifications. Briefly, 3 g seedling tissue were cross-linked in 1% formaldehyde by vacuum for 30 minutes. The chromatin was extracted on ice as described by Bowler method and sheared to 200-500 bp fragments by sonication. Subsequently, the DNA fragments were immunoprecipitated by anti-H3K18Ac (A7257, ABclonal). The ChIP DNA was eluted, purified, and dissolved in ddH2O. ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
HiSeq X Ten |
|
|
Description |
ZH11_R_H3K18Ace_1_IP
|
Data processing |
Sequencing reads were mapped to rice reference genome (MSU7) using Bowtie2. ChIP-seq peaks and the signal tracks were generated by MACS2. Assembly: MSU7 Supplementary files format and content: ChIP-seq signal tracks in bigWig format.
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Submission date |
Jun 28, 2022 |
Last update date |
May 09, 2023 |
Contact name |
Yu Chang |
E-mail(s) |
yuchang@mail.hzau.edu.cn
|
Organization name |
Huazhong Agricultural University
|
Department |
National Key Laboratory of Crop Genetic Improvement
|
Street address |
No.1, Shizishan Street, Hongshan District
|
City |
Wuhan |
State/province |
Hubei |
ZIP/Postal code |
430070 |
Country |
China |
|
|
Platform ID |
GPL23876 |
Series (1) |
GSE207132 |
Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice |
|
Relations |
BioSample |
SAMN29403211 |
SRA |
SRX15931126 |