Transcriptomics,Multiomics

Dataset Information

15

Transcription profiling by RNA-seq of seven tissues from Oryza sativa japonica Nipponbare

ABSTRACT: Expression in seven tissues from Oryza sativa L. ssp japonica Nipponbare was profiled using RNA-sequencing: callus, leaf, root, seed, shoot, panicle before flowering, and panicle after flowering. The original experiment examined gene expression in the seven tissues, and utilized the data both to compare gene expression patterns between retrogenes and their parents and to compare patterns of expression divergence between RNA-based duplicates and DNA-based duplicates Note: All samples in SRA were assigned the same sample accession (DRS000668). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

REANALYSED by: E-MTAB-2037

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Oryza Sativa Japonica Group

TISSUE(S): Callus, Pre-flowering Panicle, Root, Seed, Post-flowering Panicle, Leaf, Shoot

SUBMITTER: National Institute of Agrobiological Sciences   Brandon S Gaut   Maria C Keays 

PROVIDER: E-MTAB-2037 | ArrayExpress | 2011-12-21

REPOSITORIES: ArrayExpress

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Publications

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

Sakai Hiroaki H   Mizuno Hiroshi H   Kawahara Yoshihiro Y   Wakimoto Hironobu H   Ikawa Hiroshi H   Kawahigashi Hiroyuki H   Kanamori Hiroyuki H   Matsumoto Takashi T   Itoh Takeshi T   Gaut Brandon S BS  

Genome biology and evolution 20111031

Gene duplication occurs by either DNA- or RNA-based processes; the latter duplicates single genes via retroposition of messenger RNA. The expression of a retroposed gene copy (retrocopy) is expected to be uncorrelated with its source gene because upstream promoter regions are usually not part of the retroposition process. In contrast, DNA-based duplication often encompasses both the coding and the intergenic (promoter) regions; hence, expression is often correlated, at least initially, between D  ...[more]

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