Transcriptomics

Dataset Information

304

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


ABSTRACT: 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).

ORGANISM(S): Homo sapiens  

SUBMITTER: Katlin Fejes-Toth   Philipp Kapranov  Katalin Fejes Toth 

PROVIDER: E-GEOD-14362 | ArrayExpress | 2009-01-26

SECONDARY ACCESSION(S): SRP000599GSE14362PRJNA111397

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs.

Nature 20090125 7232


The transcriptomes of eukaryotic cells are incredibly complex. Individual non-coding RNAs dwarf the number of protein-coding genes, and include classes that are well understood as well as classes for which the nature, extent and functional roles are obscure. Deep sequencing of small RNAs (<200 nucleotides) from human HeLa and HepG2 cells revealed a remarkable breadth of species. These arose both from within annotated genes and from unannotated intergenic regions. Overall, small RNAs tended to al  ...[more]

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