LncRNAs are transcripts longer than ~200 nucleotides with little or no protein-coding capacity. There is growing evidence that lncRNAs have important function in development and disease genesis, but most of them are poorly characterized. This array is designed for profiling the Rat lncRNAs candidates and protein coding genes. While one probe designed for each coding gene is printed once, one probe for each LncRNA is printed 3 times. In addition, probes for housekeeping genes and negative probes are also printed multiple times to ensure hybridization quality. This microarray is only available for LncRNA microarray service at Arraystar.

LncRNA Data Sources: 

About 9,300 Rat lncRNAs candidates are identified from the NCBI RefSeq, UCSC all_mrna records and orthologs of mouse LncRNAs [1-9]. Highly similar sequences and ncRNAs shorter than 200 bp are excluded [10].
1. NCBI RefSeq

An increasing number of ncRNAs are acknowledged by NCBI and are collected into RefSeq database after curation. Considering the reliability of RefSeq database, we collected all the LncRNAs from this database.
2. UCSC all_mrna

2,225 mRNAs are selected from all_mrna tracks as LncRNA candidates. Sequences which have high similarity with rat coding genes are excluded. (http://genome.ucsc.edu/cgi-bin/hgTables)
3. Mouse LncRNA orthologs

Through alignment of mouse LncRNA to rat genome, we collected thousands of orthologs larger than 500 bp as rat LncRNA candidates.
4. UCRs.

Ultraconserved regions (UCRs) are considered as very important genome elements. 962 sequences derived from these regions are temporarily considered as ncRNAs.

All protein coding genes from NCBI RefSeq are also contained on this array, so that mRNAs and LncRNAs can be detected in a single experiment.

1. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J. and Wheeler D.L., (2004) GenBank: update. Nucleic Acids Res., 32, D23-D26.

2. Pruitt K.D., Tatusova T. and Maglott D.R. (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-504.

3. Hubbard T., Barker D., Birney E., Cameron G., Chen Y., Clark L., Cox T., Cuff J., Curwen V., Down T., et al. (2002) The Ensembl genome database project. Nucl. Acids Res., 2002 Jan 1;30(1):38-41.

4. Pang,K.C., Stephen,S., Engstrom,P.G., Tajul-Arifin,K., Chen,W., Wahlestedt,C., Lenhard,B., Hayashizaki,Y. and Mattick,J.S. (2005) RNAdb-a comprehensive mammalian noncoding RNA database. Nucleic Acids Res., 33, D125-D130.

5. Pang,K.C., Stephen,S., Dinger,M.E., Engstrom,P.G., Lenhard,B. and Mattick,J.S. (2007) RNAdb 2.0-an expanded database of mammalian non-coding RNAs. Nucleic Acids Res., 35, D178-D182.

6. Dinger,M.E., Pang,K.C., Mercer,T.R., Crowe,M.L., Grimmond S.M. and Mattick,J.S. (2009) NRED: a database of long noncoding RNA expression. Nucleic Acids Res., 37, D122-D126.

7. The FANTOM Consortium, et al. The transcriptional landscape of the mammalian genome. (2005)Science 309, 1559.

8. Willingham, A.T., et al. (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science, 309, 1570.

9. Calin G.A., Liu C.G., Ferracin M., Hyslop T., Spizzo R. and et al. (2007) Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12, 215-229.

10. Kent WJ. (2002) BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.