|
| Status |
Public on Sep 15, 2022 |
| Title |
BL-Hi-C_LL-ZT20-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mature leaf
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
cultivar: Minghui 63
treatment: constant light (LL)
time-point: ZT20
tissue: mature leaf
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mature rice leaves 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.
Isolated rice nuclei were digested into fragments with the MboI restriction enzyme (NEB, R0147). DNA fragments were used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no.M421F) and Klenow enzyme (NEB, cat. no. M0212L). Proximity ligation of DNA fragments was performed using a biotinylated bridge linker (forward strand:5′-[5Phos] CGCGATATC/iBIOdT/TATCTGACT-3′, reverse strand:5′-[5Phos] GTCAGATAAGATATCGCGT-3′) in situ. The protein-DNA complex was reverse cross-linked, and BL Hi-C libraries were prepared using Tn5 transposase (VAHTS; cat. no.TD501).
BL-Hi-C
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
BL-Hi-C_LL-ZT20.combine.hic
|
| Data processing |
Raw BL-Hi-C data were analyzed using the ChIA-PET pipeline
MH63 rice reference genome using BWA with up to two mismatches allowed
PETs were used for further classification as self-ligation,inter-ligation, and other PETs
interactions with an FDR < 0.05 and Paired-End Tag count (PETcount) ≥ 3 were selected for further analysis
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: The hic format file was converted by juicer_tools
|
| |
|
| Submission date |
Sep 10, 2022 |
| Last update date |
Sep 15, 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) |
| GSE213090 |
Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C] |
| GSE213227 |
Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice |
|
| Relations |
| BioSample |
SAMN30790642 |
| SRA |
SRX17525432 |
