Mouse LncRNA Expression Array V3.0

  • Description
  • Highlights
  • Database

Arraystar Mouse LncRNA Array V3.0 has a total of 35,923 lncRNAs collected from all major public databases and repositories, such as Refseq, UCSC Known Genes, Ensembl, Fantom, RNAdb , NRED, and scientific publications, and a total of 24,881 protein coding mRNAs.

Arraystar Mouse LncRNA Expression Array V3.0 is designed for the global profiling of mouse long noncoding RNAs (LncRNAs). In order to detect LncRNAs comprehensively and reliably, we updated the repertoire of LncRNAs represented on the previous Array V2.0.

The Arraystar Mouse LncRNA Expression Array V3.0 contains the following four important changes from V2.0:

1. Updated and stringent LncRNA collection. The public databases we used as the sources of our LncRNAs have been updated since the release of our V2.0 LncRNA Expression Arrays in early 2011. These databases include NCBI Refseq, UCSC Known Gene 6.0, Ensembl 38.71, Fantom3, RNAdb 2.0, and NRED. In addition, the array contains LincRNA transcripts recently identified by several laboratories and not contained in the public databases. Most importantly, we developed a stringent computational approach to identify LncRNAs from these updated databases and publications, resulting in a more reliable LncRNA collection.

2.  Concise and scientific LncRNA classification. LncRNAs have been re-classified into five subgroups (Intergenic, Bidirectional, Intronic, Antisense and Sense-overlapping) in the Arraystar Mouse LncRNA Expression Array V3.0, based on their genomic arrangements relative to nearby protein-coding genes due to non-sense mediated decay(NMD) issues. These new classifications are more concise and scientific than those described in V2.0, and will help researchers identify any putative functional relationships between LncRNAs and proximal protein-coding genes.

3.  Additional noncoding transcripts. 1,428 LncRNAs that contain an open reading frame and share the same start codon with a protein-coding transcript, but are unlikely to encode a protein, are represented on the Arraystar Mouse LncRNA Array V3.0. Further, the array contains probes for 3,419 transcribed pseudogenes.

4.  Improved transcript labeling. By using a smart labeling system, we generate Cy3-labeled RNAs along the entire length of the transcript without 3 bias. This improved labeling procedure increases the detection of RNAs in limited quantities, and minimizes the underrepresentation of certain RNA species, including degraded RNAs and RNAs lacking polyA tails, in samples.

The Arraystar Mouse Expression Array V3.0 is available only through the LncRNA Expression Array service at Arraystar. 

Product NameCatalog NoDescriptionFormatPrice
Mouse LncRNA Expression Array V3.0 AS-LNC-M-V3.0 24,881 mRNAs and 35,923 LncRNAs 8*60K

The most sensitive and best technology to profile lncRNA expression: Better than RNA-seq for lncRNA profiling as lncRNAs are often at lower abundance.

Most Extensive and Updated Coverage Available: LncRNAs are comprehensively collected from the most updated public transcriptome databases, including RefSeq, UCSC Known Genes, and Ensembl. In addition, the Arraystar Mouse LncRNA Expression Array V3.0 is designed from information contained in landmark publications [1-15].

Reliable LncRNA Collection: LncRNAs from databases and publications are filtered using a stringent computational pipeline for greater reliability.

Transcript-specific Detection: Transcript-specific probes are designed to accurately detect multiple transcript isoforms of a single gene.

Efficient and Robust Labeling System: Our "Smart" labeling system enhances the detection of both intact and degraded RNAs in limited quantities.

Systematic LncRNA Classification: Arraystar classifies LncRNAs into subgroups (Intergenic, Bidirectional, Intronic, Antisense and Sense-overlapping), aiding the identification of any putative functional relationships between LncRNAs and their associated protein-coding genes.

Data Sources
Composition of the Arraystar Mouse LncRNA Expression Array V3.0


Total Number of Distinct Probes 60,804
Probe Length 60 nt
Probe Selection Region Specific exon or splice junction probes along the entire length of the transcript
Probe Specificity Transcript-specific
Labeling Method By using a smart labeling system, we generate antisense RNAs that are Cy3- or Cy5-labeled along the entire length of the transcript without 3' bias, for both intact and degraded RNA samples in limited quantities.
Protein Coding Transcripts (mRNAs) 24,881
LncRNAs 35,923
Transcribed Pseudogenes 3,419
LncRNAs with Open Reading Frames 1,428
LncRNA Sources LncRNA collections are based on:
Updated Databases:
NCBI Refseq, UCSC Known Gene 6.0, Ensembl 38.71, Fantom3, RNAdb 2.0, and NRED;
lincRNAs[1-4], T-UCRs[5], Evolutionary constrained LncRNAs[6]
mRNA Sources mRNA collection is based on:
The collaborative consensus coding sequence (CCDS) project
Array Format 8 x 60K

Reference1.  Guttman, M., et al., Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 2009. 458(7235): p. 223-7.
2.  Khalil, A.M., et al., Many mouse large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A, 2009. 106(28): p. 11667-72.
3.  Alexander, D.R., et al., Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny In Vivo. Cell Stem Cell, 2013. 12(5):p616-28.
4.  Sigova, A.A., et al., Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A, 2013. 110(8): p. 2876-81.
5.  Bejerano, G., et al., Ultraconserved elements in the mouse genome. Science, 2004. 304(5675): p. 1321-5.
6.  Willingham, A.T., et al., A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science, 2005. 309(5740): p. 1570-3.
7.  Pruitt, K.D., T. Tatusova, and D.R. Maglott, NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res, 2005. 33(Database issue): p. D501-4.
8.  Pang, K.C., et al., RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res, 2005. 33(Database issue): p. D125-30.
9. Pang, K.C., et al., RNAdb 2.0--an expanded database of mammalian non-coding RNAs. Nucleic Acids Res, 2007. 35(Database issue): p. D178-82.
10. Carninci, P., et al., The transcriptional landscape of the mammalian genome. Science, 2005. 309(5740): p. 1559-63.
11. Dinger, M.E., et al., NRED: a database of long noncoding RNA expression. Nucleic Acids Res, 2009. 37(Database issue): p. D122-6.
12. Benson, D.A., et al., GenBank: update. Nucleic Acids Res, 2004. 32(Database issue): p. D23-6.
13. Hsu, F., et al., The UCSC Known Genes. Bioinformatics, 2006. 22(9): p. 1036-46.
14. Mercer, T.R., et al., Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A, 2008. 105(2): p. 716-21.
15. Amaral, P.P., et al., lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res, 2011. 39(Database issue): p. D146-51.