Dataset Information


The Physcomitrella Degradome

ABSTRACT: Deep sequencing of the 5' ends of uncapped, polyA-enriched mRNA from the moss Physcomitrella patens was performed (e.g. "degradome sequencing"). This GEO record contains all genome-matched and/or transcriptome-matched processed 24nt tags, representing the 5' ends of uncapped messages. These data were used to 1) discover microRNA targets and 2) to examine patterns of MIRNA hairpin cleavage. Overall design: A sample of wild-type polyA+ RNA from P. patens protonemata was used to construct a degradome library, which was subsequently sequenced using an ABI SOLiD instrument. Computational processing to trim 5' and 3' adapter sequences left 24nt tags, the 5' ends of which represented the 5' ends of uncapped mRNAs.

INSTRUMENT(S): AB SOLiD System 2.0 (Physcomitrella patens)

SUBMITTER: Michael J Axtell  

PROVIDER: GSE16367 | GEO | 2009-10-01



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A method to discover phased siRNA loci.

Axtell Michael J MJ  

Methods in molecular biology (Clifton, N.J.) 20100101

Short, interfering RNAs (siRNAs) arise from the processing of long double-stranded RNA (dsRNA) by Dicer enzymes. Dicers generate siRNA duplexes by successive hydrolysis of both strands of the dsRNA phosphodiester backbone at positions determined by measuring 21-24 nucleotides from an exposed dsRNA terminus. Therefore, a population of dsRNAs with precisely identical termini will produce siRNA spaced in regular, 21-24-nucleotide intervals. This chapter presents an easily customized and generally a  ...[more]

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