Transcriptomics,Genomics

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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

SECONDARY ACCESSION(S): SRP013556GSE38480PRJNA168014

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

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]

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