NCode™ Noncoding RNA Arrays
Accelerate discovery with the first commercially available microarrays for profiling long noncoding RNA (ncRNA). NCode™ Human and Mouse Non-coding RNA Microarrays provide first-generation high-density arrays to profile longer ncRNA (>200 bases) and to analyze mRNA simultaneously on the same array. In addition to the ncRNA content, probes targeting mRNA allow discovery of coordinated expression with associated protein-coding genes.
Profile ncRNA with your existing expression array workflow
Using the NCode™ microarrays, you can:
- Profile over 17,000 long (>200 bases) ncRNAs in human and over 10,000 ncRNAs in mouse, derived from published sources*
- Correlate ncRNA expression with mRNA expression for known pathways, with simultaneous profiling of coding and noncoding RNAs
- Perform ncRNA research using standard expression array labeling technologies and instrumentation - including the Agilent® Technologies system.
The NCode™ Human and Mouse Non-coding RNA Microarrays are available in a duplex array format in two sizes (1 slide and 5 slides).
Table 1—Each slide contains noncoding RNA and mRNA features and controls for monitoring experimental success.
|Format||Human ncRNA Array||Mouse ncRNA Array|
|Total features||22,074 coding features|
17,112 noncoding features*
|25,179 coding features|
10,802 noncoding features*
|Control features||1,325 on each array||1,325 on each array|
*The ncRNA probes predominantly target full-length cDNAs cataloged from published studies.Specifically, the ncRNA content has been developed from the following sources: manual curation from literature, Functional Annotation of Mouse (FANTOM3) project, Human Full-length cDNA Annotation Invitational (H-Invitational) project, antisense ncRNAs from cDNA and EST database for mouse and human using a computation pipeline (Engstrom et al. 2006), human snoRNAs and scaRNAs derived from snoRNA-LBME-db, RNAz (Washietl et al. 2005), Noncoding RNA Search (Torarinsson, et al. 2006), and EvoFold (Pedersen et al. 2006).
Figure 1—NCode™ Human Non-Coding RNA Array permits simultaneous detection of mRNA and ncRNA expression in biological samples. The histogram describes the observed fold change of both mRNA and ncRNA transcripts in breast cancer tumor samples vs. adjacent normal tissues in a single patient. Fold change from expression levels from normal tissue were calculated for known breast cancer associated transcripts (both coding and noncoding) derived from the tumorgene.org database.
Noncoding sequences were identified by an algorithm that scores various characteristics of protein-coding genes including open reading frame length, synonymous/nonsynonymous base substitution rates, and similarity to known proteins (see Mercer et al. 2008). Along with putative long ncRNAs, the array also targets characterized ncRNAs, such as Xist, Air, PINC, Neat1, and Neat2. Although the array targets some miRNA precursors, it is not designed to detect miRNAs. Refer to the Ncode™ miRNA products for tools optimized for miRNA labeling, arrays, and qRT-PCR.