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| Status |
Public on Sep 28, 2022 |
| Title |
DJ_H3K27me3_ChIA_Rep1 |
| Sample type |
SRA |
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| Source name |
seedling
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Dongjin
tissue: seedling
chip antibody: H3K27me3 antibodies (Abclonal, A2363)
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| 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).
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| Library strategy |
ChIA-PET |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Description |
DJ_H3K27me3_ChIA.bedpe
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| 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
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| Submission date |
Sep 23, 2022 |
| Last update date |
Sep 28, 2022 |
| Contact name |
yue li |
| E-mail(s) |
lyue@webmail.hzau.edu.cn
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| Organization name |
HUAZHONG Agriculture University
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| Street address |
Shizishan Street
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL23876 |
| 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 |
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| Relations |
| BioSample |
SAMN30985762 |
| SRA |
SRX17682532 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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