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Transcriptome profiling of various organs at different developmental stages in rice (paired-end)

ABSTRACT: To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE56462 | GEO | 2015/11/25

SECONDARY ACCESSION(S): PRJNA243368

REPOSITORIES: GEO

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Transcriptome profiling of various organs at different developmental stages in rice (paired-end)

Project description:To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

2015-11-25 | E-GEOD-56462 | biostudies-arrayexpress

Transcriptome profiling of various organs at different developmental stages in rice (single-end)

2015-11-25 | GSE56463 | GEO

Transcriptome profiling of various organs at different developmental stages in rice (single-end)

Project description:To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using stranded single-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

2015-11-25 | E-GEOD-56463 | biostudies-arrayexpress

Transcriptome profiling of noncoding RNAs in maize (paired-end)

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Transcriptome profiling of noncoding RNAs in maize (paired-end)

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rice whole transcriptome surveyed by RNA-Seq and Paired-end technology

Project description:Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations Keywords: Expression profiling by high throughput sequencing

2010-03-01 | GSE16631 | GEO

rice whole transcriptome surveyed by RNA-Seq and Paired-end technology

2010-03-01 | E-GEOD-16631 | biostudies-arrayexpress

Spatio-temporal gene expression of various tissues/organs throughout entire growth in rice

2011-01-13 | GSE21396 | GEO

Spatio-temporal gene expression of various tissues/organs throughout entire growth in rice

Project description:An overview of the expression pattern of all rice genes under natural field conditions based on microarray analysis of different organs and tissues at various stages of growth and development from transplanting to harvesting. A total of 48 samples representing organs/tissues at various stages of growth and development with 3 replicates each except for one anther sample with 2 replicates. Vegetative organs such as leaf blade, leaf sheath, root and stem were sampled during the vegetative, reproductive and ripening stages. Young inflorescence, anther, pistil, lemma, palea, ovary, embryo, and endosperm were sampled at various stages of development.

2011-01-13 | E-GEOD-21396 | biostudies-arrayexpress

Expression data from rice organs at the reproductive stage

Project description:Plant hormones interact with each other and regulate gene expression to control plant growth and development. To understand the complex network, accumulation of comprehensive and integrative data of gene expression and hormone concentration is important. Using microarray, global gene expression profile was analyzed to compare with plant hormone concentration in 14 parts of rice at reproductive stage. The microarray data are used to construct public rice hormonome-transcriptome database UniVIO (http://univio.psc.riken.jp/).

2012-10-13 | GSE41556 | GEO

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