#25 DASHR human small RNA database

[Anonymous]

Database:
http://lisanwanglab.org/DASHR

Reference:
DASHR: database of small human non-coding RNAs. NAR Database Issue, 2016 [Epub ahead of print].
http://www.ncbi.nlm.nih.gov/pubmed/26553799

Contact:
dashr@lisanwanglab.org

Category:
RNA sequence database

Description:
DASHR, the database of human small non-coding RNAs (sncRNAs), integrates 187 smRNA high-throughput sequencing (smRNA-seq) datasets with over 2.5 billion reads and annotation data for all major classes of small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs).
DASHR contains the most comprehensive information (sequence, annotation, sequencing-based expression, RNA secondary structure, and evidence of specific RNA processing) to date on both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs in over 40 human tissues. The database is publicly available at http://lisanwanglab.org/DASHR and the corresponding DASHR UCSC Genome Browser hub
http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=http://tesla.pcbi.upenn.edu/DASHR/tracks/hub.txt

DASHR UCSC Genome Browser Hub URL: http://lisanwanglab.org/DASHR/tracks/hub.txt

Example usage cases:
Documented in detail on the DASHR website and in the paper (http://www.ncbi.nlm.nih.gov/pubmed/26553799)

Some of the examples are:

A. RNA search:
DASHR allows search by the full or partial name of sncRNA gene or mature RNA product, locate sncRNA loci overlapping with the given genomic interval coordinates, or query sncRNA records in the database by RNA sequence.
Search by RNA name accepts HGNC symbol, RefSeq ID, UCSC ID, small RNA name, or gene name:
primary miRNA search: MIR192, hsa-mir-192, NR_029578, uc010rnr.1
mature miRNA 3p/5p search: hsa-miR-192-3p, hsa-miR-192-5p
snoRNA/snRNA search: U14, HBII-251, SNORD85, NR_003066, uc001bsl.1
scRNA search: HY1, RNY1
tRNA search: tRNA22, chr14.tRNA22-ProAGG, uc021rnx.1
piRNA search: piR-36025
tRNA fragment search (tRF-3p/tRF-5p): chr14.tRNA22-ProAGG-tRF3

B. Expression data browser: http://lisanwanglab.org/DASHR/smdb.php#tabBrowse

sncRNA genes:
http://lisanwanglab.org/DASHR/show-expression-table.php?start=0

mature sncRNA products:
http://lisanwanglab.org/DASHR/browse-peak-table.php?start=0

Expression data browser aims to answer questions such as:
1. What is the expression pattern for hsa-mir-200a miRNA gene and its mature products (hsa-mir-200a-5p or hsa-mir-200a-3p) in normal tissues?
2. What are the sncRNA genes and mature sncRNA products expressed in human brain?
3. What annotated sncRNAs are in the specific genomic location and how are they expressed in specific tissue/cell type or across all tissues and cell types?

C. Data visualization/download:
The genome-wide map of small RNA loci, raw signal track data, sncRNA contigs (called peaks), sequences, and annotations can be
1) downloaded from the database website http://lisanwanglab.org/DASHR/smdb.php#tabDownload,
2) accessed via the UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=http://tesla.pcbi.upenn.edu/DASHR/tracks/hub.txt
3) accessed through Table Browser http://genome.ucsc.edu/cgi-bin/hgTables

D. Direct access to individual RNA records:
E.g., mir-200b
http://lisanwanglab.org/DASHR/get_bg_smrna.php?coord=chr1:1102484-1102578:pos&rnaID=hsa-mir-200b

[Nick Juty]

Being followed up through email.