RNAdb

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]