DASHR - Database of small human noncoding RNAs

DASHR (Database of small human non-coding RNAs) is a database developed at the University of Pennsylvania with the most comprehensive expression and processing information to date on all major classes of human small non-coding RNA (sncRNA) genes and mature sncNA annotations, expression levels, sequence and RNA processing information across 185 human tissues, cell types, and cell lines.
The content of the database derives from integrating annotation data with curation, annotation, and computational analysis of 802 small-RNA (smRNA-seq) deep sequencing datasets with over 22 billion reads from >60 independent studies.

DASHR v2.0

Samples per data collection

DASHR1 GEO
DASHR2 GEO
ENCODE portal
ENCODE GEO

Biosample types

cell line
cell type
immortalized cell line
in vitro differentiated cells
induced pluripotent stem cell line
primary cell
stem cell
tissue

Platform types

HiSeq 2000
Genome Analyzer
Genome Analyzer II
Genome Analyzer IIx
HiScanSQ
HiSeq 1500
HiSeq 2000
HiSeq 2500
MiSeq
NextSeq 500

DASHR v2.0 data collection contains 802 datasets (>22 billion reads) across 86 tissues, 51 cell types and 48 cell lines, with all annotation and expression information additionally accessible in UCSC Genome Browser for both GRCh37/hg19 (DASHR v2.0 GRCh37/hg19) and GRCh38/hg38 (DASHR v2.0 GRCh38/hg38) human genome builds.

DASHR v2.0 release integrates:

4 times more sncRNA experiments across multiple data collections and RNA-seq protocols, including 34 new GEO/SRA small RNA-seq studies (365 experiments) and all 240 ENCODE short total RNA-sequencing experiments;
both GRCh37/hg19 and GRCh38/hg38 sncRNA annotation and expression information;
13 times more annotated and 372,194 novel sncRNA loci (1,678,800 total);
enhanced user interface for selecting sncRNA datasets, browsing and filtering of sncRNA loci;
3,280,375 annotations for non-small RNA genes and other genomic elements (long-noncoding RNAs, mRNAs, promoters, and repeat elements).

Release notes

Getting Started

To get started, click on the Search to search small RNA by name/ID, genomic coordinates, sequence, or click Browse to explore small RNA expression and annotation information. Use Download to download DASHR expression and annotation data.

Citation

If you use DASHR in your research or publications, please cite:

Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung. DASHR v2.0: database of small human noncoding RNAs in human tissues and cell types. Bioinformatics, 2018 doi.org/10.1093/bioinformatics/bty709

Yuk Yee Leung*, Pavel P. Kuksa*, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, and Li-San Wang. DASHR: database of small human noncoding RNAs. Nucl. Acids Res., 2016 (Database Issue) doi:10.1093/nar/gkv1188

Funding

National Institute of General Medical Sciences [R01-GM099962]; National Institute on Aging [U54-AG052427, U01-AG032984, U24-AG041689, UF1-AG047133], National Institute on Aging [T32-AG00255].