deepBase

RNA Type: Multiple classes

Overview: deepBase is a resource of next generation sequencing data of small RNA libraries using different technological platforms obtained from several model organisms (Homo sapiens, Mus musculus, Gallus gallus, Ciona intestinalis, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana). It stores information related to different small and long RNA classes.

Search Methods:

• Similarity: search by the exact read sequence extracted from deep sequencing data, or by similarity search against the seven genomes. The BLAST program is used for similarity searches.
• Keyword: search by ncRNA name or by minimum read number.
• TAG: search by ncRNA Type, organism/clade/genome, database and by small RNA library.
• Genomic Location: search by chromosome location and organism. Searches can be restriced to a specific ncRNA type (e.g. rasRNA, pasRNA or easRNA).
• Density of ncRNAs: search using the genomic location or by organism and minimum read number.

Source: Literature, NCBI GEO, Ensembl, UCSC, miRBase, snoRNABase (Human), Plant snoRNA Database (Arabidopsis), Genomic tRNA Database, The Arabidopsis Information Resource (TAIR), prediction tools (miRDeep, snoSeeker).

Information Source: Experimental, In silico annotation, Literature.

Information Content: Annotation, Cell type, Cluster, Expression, Next-generation data, Other RNAs, Platform, Prediction tools, Reads, Sequence, small RNA Library, Tissue.

Reference: Yang et al., 2010

PubmedID: 19966272.

Year: 2010

Multiple search: Yes

Download: BED, FASTA.

Genomic Overview: Yes

Organism: Homo sapiens (Human), Mus musculus (House Mouse), Gallus gallus (Chicken), Ciona intestinalis, Drosophila melanogaster (Common Fruit Fly), Caenorhabditis elegans, Arabidopsis Thaliana (Thale Cress).

Url: http://deepbase.sysu.edu.cn/