Dataset Information


Transcriptome and methylome interactions in rice hybrids

ABSTRACT: This research reports genome-wide measurements of genetic and epigenetic patterns of inheritance through an integrative analysis of BS-seq, RNA-seq, and siRNA-seq data in two inbred parents of the Nipponbare (NPB) and Indica (93-11) variety of rice and their hybrid offspring. We generated integrative maps of whole genome cytosine methylation profiles (BS-Seq), transcriptional profiles (RNA-seq), and small RNA profiles (sRNA-seq) to characterize two rice subspecies, Oryza sativa spp japonica (Nipponbare) and Oryza sativa spp indica (93-11) and their two reciprocal hybrid offspring using Illumina's sequencing-by-synthesis (SBS) platform .

ORGANISM(S): Oryza sativa Indica Group  

SUBMITTER: David Lopez   Suhua Feng  Blake C Meyers  Steve Jacobsen  Yulin Jia  Chodavarapu Ramakrishna  Bo Ding  Stacey A Simon  Guo-Liang Wang  Blake C. Meyers  Matteo Pellegrini 

PROVIDER: E-GEOD-38480 | ArrayExpress | 2012-07-10



altmetric image


Transcriptome and methylome interactions in rice hybrids.

Chodavarapu Ramakrishna K RK   Feng Suhua S   Ding Bo B   Simon Stacey A SA   Lopez David D   Jia Yulin Y   Wang Guo-Liang GL   Meyers Blake C BC   Jacobsen Steven E SE   Pellegrini Matteo M  

Proceedings of the National Academy of Sciences of the United States of America 20120709 30

DNA methylation is a heritable epigenetic mark that controls gene expression, is responsive to environmental stresses, and, in plants, may also play a role in heterosis. To determine the degree to which DNA methylation is inherited in rice, and how it both influences and is affected by transcription, we performed genome-wide measurements of these patterns through an integrative analysis of bisulfite-sequencing, RNA-sequencing, and siRNA-sequencing data in two inbred parents of the Nipponbare (NP  ...[more]

Similar Datasets

2014-09-11 | E-GEOD-42314 | ArrayExpress
2010-07-18 | E-MTAB-275 | ArrayExpress
2012-02-01 | E-GEOD-27856 | ArrayExpress
2015-09-01 | E-GEOD-57706 | ArrayExpress
2016-04-13 | E-GEOD-67373 | ArrayExpress
2009-02-08 | E-GEOD-11966 | ArrayExpress
2014-08-17 | E-GEOD-51468 | ArrayExpress
2017-03-29 | PXD004417 | Pride
2010-01-01 | E-GEOD-19050 | ArrayExpress
2012-02-19 | E-GEOD-31077 | ArrayExpress