 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 15, 2014 |
| Title |
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine in rice |
| Organism |
Oryza sativa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We generated a genome-wide map of 5hmC in rice panicle using a sensitive chemical labeling method to capture DNA fragments with 5hmC modification, followed by NGS sequencing. We showed that the 5hmC peaks distribution is non-random, about 52% 5hmC was located in gene bodies, 25% in intergenic regions, 11% in promoters, and 12% in immediate downstream. It was significantly enriched in heterochromatic regions of chromosomes 4 and 10, and especially located around TE genes. Combined with RNA-seq transcriptome data, we found that the gene-specific alterations of 5hmC can result in gene activation or repression, suggesting a potential role for 5hmC in gene regulation. From the compared distribution analysis among super-hybrid rice cultivars LYP9, and its parental lines 93-11 and PA64s, we investigated the cultivar-specificity of both the global levels and locus-specific distribution of 5hmC. Our data provided an overview of the genomic distribution of 5hmC in rice panicle. This will set the stage for further functional characterization of this novel DNA modification and its biosynthesis in rice.
|
| |
|
| Overall design |
Examination of 5hmC modifications in rice panicle
This submission represents ChIP-Seq component of study.
|
| |
|
| Contributor(s) |
Song S |
| Citation(s) |
26272901 |
| |
| Submission date |
Apr 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shuhui Song |
| E-mail(s) |
songshh@big.ac.cn
|
| Organization name |
Beijing Institute of Genomics, Chinese Academy of Sciences
|
| Street address |
No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China
|
| City |
Beijing |
| ZIP/Postal code |
86 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL13160 |
Illumina HiSeq 2000 (Oryza sativa) |
|
| Samples (3) |
|
| Relations |
| BioProject |
PRJNA159185 |
| SRA |
SRP012187 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37242_RAW.tar |
210.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
