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RNAdb specifications

Information


Unique identifier OMICS_04872
Name RNAdb
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 2.0
Maintained No

Maintainer


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Publications for RNAdb

RNAdb citations

 (30)
call_split

Coding and noncoding landscape of extracellular RNA released by human glioma stem cells

2017
Nat Commun
PMCID: 5658400
PMID: 29074968
DOI: 10.1038/s41467-017-01196-x
call_split See protocol

[…] ore than 10% mismatched nucleotides were excluded. The remaining reads were mapped to spike-ins (UniSp2, UniSp4 and UniSp5; parameter: -v 1 --all), and other non-coding RNA classes including tRNAs (gtRNAdb), piRNAs (RNAdb), snoRNA (snoRNA-LBME-db), scRNAs (Genbank), and others (Rfam database) (parameter: -v 2 --all). Finally, the remaining reads were mapped to the hg19 human genome, and the reads […]

library_books

Microarray expression profile analysis of long non coding RNAs in optineurin E50K mutant transgenic mice

2017
PMCID: 5561974
PMID: 29067446
DOI: 10.3892/mmr.2017.6722

[…] transcripts, performed by KangChen Biotech Co., Ltd. (Shanghai, China). This microarray contains 35,923 lncRNAs collected from the National Center for Biotechnology Information Refseq, UCSC, Ensembl, RNAdb 2.0, Fantom3, ncRNA expression databases, and from previous literature. A total of 24,881 coding transcripts were extracted based on the Collaborative Consensus Coding Sequence (CCDS) public sou […]

library_books

High expression of the long non coding RNA HEIRCC promotes Renal Cell Carcinoma metastasis by inducing epithelial mesenchymal transition

2016
Oncotarget
PMCID: 5351652
PMID: 28030807
DOI: 10.18632/oncotarget.14149

[…] 40,916 lncRNAs were collected from authoritative data sources, including the GENCODE/Ensembl, Human LncRNA Catalog, RefSeq, USCS, ncRNA Expression Database (NRED), H-InvDB, LncRNAs-a (enhancer-like), RNAdb, CombinedLit, Antisense ncRNA pipeline, HoxncRNAs, UCRs, and Chen Runsheng lab. After hybridization and washing, the processed slides were scanned with the Agilent Microarray Scanner (Agilent te […]

library_books

A Review of Computational Methods for Finding Non Coding RNA Genes

2016
Genes
PMCID: 5192489
PMID: 27918472
DOI: 10.3390/genes7120113

[…] RNAs (tRNAs) and ribosomal RNAs (rRNAs). It also introduced a classification system termed process function class (PfClass) based on the cellular processes and functions associated with the ncRNA.The RNAdb [] was launched as a sequence repository for experimentally supported regulatory mammalian ncRNAs (miRNAs, small nucleolar RNAs (snoRNAs), but not tRNAs, rRNAs, and spliceosomal RNAs). Apart fro […]

library_books

Highly sensitive sequencing reveals dynamic modifications and activities of small RNAs in mouse oocytes and early embryos

2016
Sci Adv
PMCID: 4974095
PMID: 27500274
DOI: 10.1126/sciadv.1501482

[…] of piRNA was calculated by mapping the reads to the previously annotated piRNA libraries from four databases: piRNABank (http://pirnabank.ibab.ac.in/), RNA database (http://jsm-research.imb.uq.edu.au/rnadb), the Gene Expression Omnibus database (GSE7414), and GenBank (ftp://ftp.ncbi.nih.gov/genbank/). To identify other repetitive element–derived small RNAs, small RNAs that did not belong to the pi […]

library_books

Diverse human extracellular RNAs are widely detected in human plasma

2016
Nat Commun
PMCID: 4853467
PMID: 27112789
DOI: 10.1038/ncomms11106

[…] to the provided miRNA library, reads that did not align in any of the previous steps are mapped against a variety of small-RNA libraries including (with no significance to the ordering): tRNAs from gtRNAdb, piRNAs from RNAdb, snoRNAs from snoRNA-LBME-db and snRNAs and other RNA sequences from RFam. In both steps 3 and 4 reads were allowed to multi-map to different annotated transcripts and in case […]

Citations

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RNAdb institution(s)
ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; T cell Laboratory, Ludwig Institute for Cancer Research, Melbourne Centre for Clinical Sciences, Austin Hospital, Heidelberg, VIC, Australia; Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway; Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
RNAdb funding source(s)
Supported by funding from the Australian National Health & Medical Research Council, the Foundation for Research, Science and Technology, New Zealand, the Australian Research Council, the Queensland State Government and the University of Queensland and the Functional Genomics Programme (FUGE) of the Research Council of Norway.

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