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E-GEOD-14362 - Genome-wide annotation of small RNAs expressed in HeLa and HepG2 cells

Status
Released on 26 January 2009, last updated on 27 June 2012
Organism
Homo sapiens
Samples (40)
Protocols (5)
Description
We report an applicaton of small RNA sequencing using high throughput next generation sequencing to identify the small RNA content of cell lines. By sequencing over 30 million reads we could identify a new class of small RNAs previousy observed with tiling arrays and mapping to promoter regions of coding genes. We also identified a large number of small RNAs corresponding to internal exons of coding genes. By using different enzymatic treatments and immunoprecipitation experiments, we have determined that both the promoter associated small RNAs as well as ones within the body of the genes bear 5' cap structures. Examination of the expression of small RNAs (<200nt).
Experiment type
RNA-seq of non coding RNA 
Contacts
Katalin Fejes Toth <fejes@cshl.edu>, Katlin Fejes-Toth, Philipp Kapranov
Citation
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Affymetrix ENCODE Transcriptome Project, Cold Spring Harbor Laboratory ENCODE Transcriptome Project. , PMID:19169241
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-14362.idf.txt
Sample and data relationshipE-GEOD-14362.sdrf.txt
Processed data (1)E-GEOD-14362.processed.1.zip
Additional data (1)E-GEOD-14362.additional.1.zip
Links