Transcriptomics

Dataset Information

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Identification of soybean seed developmental stage specific and tissue specific miRNA targets by degradome sequencing .


ABSTRACT: Five degradome libraries were constructed from three different seed developmental stages. Separate degradome libraries were constructed for seed coat and cotyledons to identify the tissue specific miRNAs and their potential targets. Sequencing and analysis of degradome libraries gives identification of 183 different targets for 80 known soybean miRNAs. We found 30 cotyledon specific, 18 seed coat specific and 32 miRNAs found in both tissues irrespective of the developmental stages. One interesting observation is that we found more miRNA targets in late seed developmental stages than earlier stages. Additionally, we have validated four different auxin response factor genes as targets for gma-miR160 via RNA ligase mediated 5′ rapid amplification of cDNA ends (RLM-5′RACE). GO analysis indicated the enrichment of miRNA target genes in seed development. Construction of degradome libraries using cotyledons and seed coats from 3 different developmental stages

ORGANISM(S): Glycine max  

SUBMITTER: Md Shamimuzzaman   Lila O Vodkin  Lila O. Vodkin 

PROVIDER: E-GEOD-34433 | ArrayExpress | 2012-08-07

SECONDARY ACCESSION(S): GSE34433SRP009822PRJNA149623

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing.

Shamimuzzaman Md M   Vodkin Lila L  

BMC genomics 20120716


BACKGROUND: MicroRNAs (miRNAs) regulate the expression of target genes by mediating gene silencing in both plants and animals. The miRNA targets have been extensively investigated in Arabidopsis and rice using computational prediction, experimental validation by overexpression in transgenic plants, and by degradome or PARE (parallel analysis of RNA ends) sequencing. However, miRNA targets mostly remain unknown in soybean (Glycine max). More specifically miRNA mediated gene regulation at differen  ...[more]

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