|
| Status |
Public on Sep 28, 2022 |
| Title |
MH_seedling_H3K27me3_ChIA_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
cultivar: Minghui 63
tissue: seedling
chip antibody: H3K27me3 antibodies (Abclonal, A2363)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rice tissues were dual cross-linked with 1% formaldehyde (SIGMA, F8775) for 10 min and 1.5 mM ethylene glycol bis (succinimidylsuccinate) (Thermo Fisher Scientific, 21565) for 30 min at 25 ℃, after which glycine was added to a final concentration of 0.2 M to stop the cross-linking reaction.
pl-DNA was end-repaired, A-tailed, and proximity ligated using a single biotinylated bridge-linker (Forward strand: 5′-[5Phos]CGCGATATC/iBIOdT/TATCTGACT-3′, Reverse strand: 5′-[5Phos]GTCAGATAAGATATCGCGT-3′). Proximity ligated protein-DNA complexes were eluted and reverse cross-linked (similar to that in eChIP-Seq). Tn5 transposase (VAHTS， TD501) was used to prepare ChIA-PET libraries according to the operation manual, and the libraries were sequenced (paired end 150 bp) using an Illumina HiSeq X-Ten (AnnoRoad Company, Beijing, China).
|
| |
|
| Library strategy |
ChIA-PET |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
MH_seedling_H3K27me3_ChIA.bedpe
|
| Data processing |
Raw ChIA-PET data were analysed using the ChIA-PET pipeline
PETs were used for further classification as self-ligation,inter-ligation, and other PETs
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: cluster.bedpe file was filtered with false discovery (FDR) > 0.05
|
| |
|
| Submission date |
Sep 23, 2022 |
| Last update date |
Sep 28, 2022 |
| Contact name |
yue li |
| E-mail(s) |
lyue@webmail.hzau.edu.cn
|
| Organization name |
HUAZHONG Agriculture University
|
| Street address |
Shizishan Street
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL26667 |
| Series (2) |
| GSE214050 |
3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIA-PET] |
| GSE214073 |
3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice |
|
| Relations |
| BioSample |
SAMN30985770 |
| SRA |
SRX17682524 |
