Genomics

Dataset Information

15

Short RNA profiling of ES cells with and without Dicer


ABSTRACT: To better understand Dicer function, and the potential mechanisms by which RNAi contributes to pluripotency, short RNA expression was profiled from 4 ES cell libraries: 2 made from a Dicer-conditional ES cell line before and several months after deletion of Dicer, and 2 made before and 5 days after demethylation of J1 ES cells with 5-aza-deoxycytidine. Contributed here are the unannotated sequence data from each library, including those sequences that did not match the mouse genome or any known non-coding RNAs. Keywords: 454 sequencing, miRNA, dicer, demethylation Overall design: cDNA libraries were made as described in Neilson et al. Genes and Development, 2007 Mar 1;21(5):578-89.

INSTRUMENT(S): MIT/SharpLab Mouse ES cell 454 2007

SUBMITTER: J. Mauro Calabrese   

PROVIDER: GSE9306 | GEO | 2007-10-31

SECONDARY ACCESSION(S): PRJNA102957

REPOSITORIES: GEO

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Publications

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.

Calabrese J Mauro JM   Seila Amy C AC   Yeo Gene W GW   Sharp Phillip A PA  

Proceedings of the National Academy of Sciences of the United States of America 20071107 46


Short RNA expression was analyzed from Dicer-positive and Dicer-knockout mouse embryonic [corrected] stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can be accounted for by six distinct miRNA loci. Four of these miRNA loci or their human homologues have demonstrated roles in cell cycle regulation or oncogenesis, suggesting that a major function of the  ...[more]

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