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| Status |
Public on Jul 01, 2021 |
| Title |
Characterization of G-quadruplexes in the rice genome |
| Organism |
Oryza sativa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure functioning in various biological processes in mammals. G4 ChIP-seq assay, In this study, we developed a robust BG4-DNA ChIP-seq for global identification of DNA G4 in rice..We found that G4s harbored some functional motifs for binding of certain trans-factors, were co-localized with R-loops and DHSs in the rice genome. Importantly, G4s exhibited differential effects on DNA methylation between TE and non-TE genes in rice. Especially, G4 intensity-dependent enrichment occurred between DNA 5mC and 6mA.These DNA-related features suggest potential regulatory roles of G4 in rice. Thus, our study will pave the way for prompting intensive characterization towards identifying novel functions of G4 in plants, especially for agronomic important crops.
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| Overall design |
Two BG4-ChIP-seq biological replicates libraries, input library, high resolution sequencing using Illumina HiSeq 2500
Two BioTASQ-ChIP biological replicates libraries, two biotin control libraries, sequenced using Illumina NovaSeq 6000
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| Contributor(s) |
Zhang P, Feng Y, Zhang W |
| Citation(s) |
37250775 |
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| Submission date |
Jun 14, 2019 |
| Last update date |
Aug 10, 2023 |
| Contact name |
Pengyue Zhang |
| E-mail(s) |
zhangpy195@163.com
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| Organization name |
NanJing Argriculture University
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| Street address |
No.1, Weigang Street, Xuanwu District, Nanjing
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platforms (2) |
| GPL19290 |
Illumina HiSeq 2500 (Oryza sativa) |
| GPL27660 |
Illumina NovaSeq 6000 (Oryza sativa) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA548958 |
| SRA |
SRP201492 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE132775_PQS_Chr10_info.xlsx |
5.7 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr11_info.xlsx |
6.8 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr12_info.xlsx |
6.5 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr1_info.xlsx |
10.8 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr2_info.xlsx |
8.6 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr3_info.xlsx |
9.0 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr4_info.xlsx |
9.0 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr5_info.xlsx |
7.6 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr6_info.xlsx |
7.7 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr7_info.xlsx |
7.3 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr8_info.xlsx |
7.0 Mb |
(ftp)(http) |
XLSX |
| GSE132775_PQS_Chr9_info.xlsx |
5.7 Mb |
(ftp)(http) |
XLSX |
| GSE132775_RAW.tar |
715.4 Mb |
(http)(custom) |
TAR (of BED, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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