|
| Status |
Public on Sep 15, 2022 |
| Title |
ChIP-Seq_DD-ZT12-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mature leaf
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
cultivar: Minghui 63
treatment: constant dark (DD)
time-point: ZT12
tissue: mature leaf
chip antibody: H3K9ac (Abcam, AB10812)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rice tissues were crosslinked with 1% formaldehyde and quenched with 0.2 M glycine.
0.5 to 1g of the sample was ground into a fine powder in liquid nitrogen, the chromatin was fragmented into 200-600 bp by ultrasound processing using Bioruptor (Diagenode). The lysates were incubated at 4 °C for 1 to 6 h and rotated to form antibody-bead complexes. After reverse cross-linking of DNA and protein, ChIP-DNA was extracted using phenol: chloroform: isoamyl alcohol (P3803; Sigma-Aldrich). ChIP-DNA libraries were prepared by Illumina® (New England BioLabs, E7645) using the NEBNext® Ultra™ II DNA Library Preparation Kit. AMPure XP beads (Beckman, A63881) were used to select 250-650 bp library fragments.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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: bogWig file by deepTools bamCoverage
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Sep 17, 2022 |
| 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) |
| GSE213226 |
Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq] |
| GSE213227 |
Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice |
|
| Relations |
| BioSample |
SAMN30815475 |
| SRA |
SRX17539487 |
