DeepBase -- Deep Sequencing Database
What you can do:
Find information about small RNAs from transcriptomic data.
Highlights:
- DeepBase is a database developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data.
- The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana.
- By analyzing approximately 14.6 million unique reads that perfectly mapped to more than 284 million genomic loci, the following were annotated and identified: approximately 380,000 unique ncRNA-associated small RNAs (nasRNAs), approximately 1.5 million unique promoter-associated small RNAs (pasRNAs), approximately 4.0 million unique exon-associated small RNAs (easRNAs) and approximately 6 million unique repeat-associated small RNAs (rasRNAs).
- 2038 miRNA and 1889 snoRNA candidates were predicted by miRDeep and snoSeeker.
- All of the mapped reads can be grouped into about 1.2 million RNA clusters.
- For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display.
Keywords:
- small RNA
- miRNA
- microRNA
- snoRNA
- Small nucleolar RNA
- Small nuclear RNA
- snRNA
- promoter-associated small RNA
- pasRNA
- exon-associated small RNA
- easRNA
- repeat-associated small RNA
- rasRNA
- human
- homo sapien
- mouse
- mus musculus
- chicken
- ciona intestinalis
- drosophila melanogaster
- caenhorhabditis elegans
- arabidopsis thaliana
- c. elegans
Literature & Tutorials:
This record last updated: 01-13-2010