GSE9306
GSE GEOShort RNA profiling of ES cells with and without Dicer
Organism:
Mus musculus
Platform:
GPL5986
Samples:
4
Experiment Types:
Expression profiling by high throughput sequencing
Methylation profiling by array
Submitted:
Oct 12 2007
Last Updated:
Mar 17 2012
Status:
Public on Oct 31 2007
Contact:
J. Mauro,,Calabrese (MIT)
Relations
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA102957
Summary
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.
Analysis (2 steps)
View Data Processing
Processing steps for GSE9306
- Sequences were extracted from 454 reads that had 10 bp of perfect match to the ligated adaptors (measuring from the 3' end of the 5' adaptor and 5' end of the 3' adaptor).
- 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.
Dataset Citations (1)
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.
PMID 17989215
· 2007
· Proceedings of the National Academy of Sciences of the United States of America
J Mauro Calabrese, Amy C Seila, Gene W Yeo, Phillip A Sharp
Linked Publications (1)
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.
Proceedings of the National Academy of Sciences of the United States of America · 2007