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E-GEOD-57706 - Genome-wide maps of DNA methylation state in rice embryo and endosperm

Released on 1 September 2015, last updated on 5 September 2015
Oryza sativa
Samples (13)
Protocols (4)
We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development. Rice embryo and endosperm were selected for DNA extraction and methylacytosine immunoprecipetation combined with Illumina sequencing. We sought to obtain the genome-wide DNA methylation profilings of embryo at 3,6,9 days after pollination(DAP) and endosperm at 2,3,6,9 DAP. To that end, we hand-selected embryo at 3,6,9 DAP and endosperm at 2,3,6,9 DAP according to morphological criteria.
Experiment type
methylation profiling by high throughput sequencing 
Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development. Xing MQ, Zhang YJ, Zhou SR, Hu WY, Wu XT, Ye YJ, Wu XX, Xiao YP, Li X, Xue HW.
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-57706.idf.txt
Sample and data relationshipE-GEOD-57706.sdrf.txt
Processed data (1)