• Description
  • Highlights
  • Database
Product NameCatalog NoDescriptionFormatPrice
Rat LncRNA Expression Microarray V2.0 AS-LNC-R-V2.0 24,626 mRNAs and 13,611 lncRNAs 4*44K

Rats are a model organism of human disease and physiology in important ways. To empower LncRNA expression profiling in rats, Arraystar Rat LncRNA Expression Microarray V2.0 has updated the repertoire of LncRNAs represented on the previous Microarray version. The two major changes include:
 
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 V1.0 LncRNA Expression microarrays in early 2011. These databases include NCBI Refseq, Ensembl 5.0.79, and lncRNAdb. In addition, T-UCRs recently identified by several laboratories but not in the public databases are included. 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 Rat LncRNA Expression Microarray V2.0, based on their genomic arrangements relative to nearby protein-coding genes. The new classifications are more concise and scientifically accurate than those described in V1.0 to help researchers identify any putative functional relationships between LncRNAs and proximal protein-coding genes.

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

• Most Extensive and Updated Coverage Available: LncRNAs are comprehensively collected from the most updated public transcriptome databases, including RefSeq [1], Ensembl [2],lncRNAdb [3], and landmark publications [4-8].

• Reliable LncRNA Collection: LncRNAs from the 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 gene.

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

Data Sources 

Composition of the Arraystar Rat LncRNA Expression Microarray V2.0

Specifications

Total Number of Distinct Probes 38,237
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) 24,626
LncRNAs 13,611
Transcribed Pseudogenes 2,140
LncRNAs with Open Reading Frames 1,428
LncRNA Sources LncRNA collections are based on: Updated Databases: NCBI Refseq[1], Ensembl 5.0.79[2], lncRNAdb[3]; Literature[4-8]: T-UCRs, Evolutionary constrained LncRNAs
mRNA Sources mRNA collection is based on:
NCBI Refseq[1], Ensembl 5.0.79[2]
Array Format 4 x 44K
 

Reference

1.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.
2.Cunningham, F., M. R. Amode, et al., Ensembl 2015. Nucleic Acids Res 2015 43(Database issue): D662-669.
3.Amaral, P.P., et al., lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res, 2011. 39(Database issue): p. D146-51.
4.Bejerano, G., et al., Ultraconserved elements in the human genome. Science, 2004. 304(5675): p. 1321-5.
5.Rinn, J.L., et al., Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 2007. 129(7): p. 1311-23.
6.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.
7.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.
8.Benson, D.A., et al., GenBank: update. Nucleic Acids Res, 2004. 32(Database issue): p. D23-6.