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Degradome sequence data

ABSTRACT: To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline.

ORGANISM(S): Glycine max

PROVIDER: GSE72903 | GEO | 2017/05/01

SECONDARY ACCESSION(S): PRJNA295299

REPOSITORIES: GEO

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degradome sequence data

Project description:To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline. 4 degradome mixed samples, no replicates, but every degradome data consists of two parts data. Please note that every degradome sample has two processed and two raw data files. To have enough data, additional sequencing was performed from each sample library. And each sample raw data was processed separately (tissue_name*degradome.txt) and also combined (all_degradome*.txt).

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Project description: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

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