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Series GSE60288 Query DataSets for GSE60288
Status Public on Dec 31, 2015
Title Single-base resolution DNA methylation maps of rice cultivars under control and stress conditions
Organism Oryza sativa
Experiment type Methylation profiling by high throughput sequencing
Summary In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants.
 
Overall design Whole genome bisulfite sequencing of seven control/stressed samples from three rice cultivars (IR64, N22 and Pokkali)
 
Contributor(s) Mukesh J, VVS Narayana C, Rama S, Rohini G
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Submission date Aug 11, 2014
Last update date May 15, 2019
Contact name Mukesh Jain
Phone 91-11-26704686
Organization name Jawaharlal Nehru University
Street address New Mehrauli Road
City New Delhi
State/province New Delhi
ZIP/Postal code 110067
Country India
 
Platforms (1)
GPL13160 Illumina HiSeq 2000 (Oryza sativa)
Samples (7)
GSM1470316 IR64-Control [methylation]
GSM1470317 N22-Control [methylation]
GSM1470318 PK-Control [methylation]
Relations
BioProject PRJNA257965
SRA SRP045419

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60288_RAW.tar 803.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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