The Arraystar Human LncRNA Microarray V2.0 is designed for the global profiling of human LncRNAs and protein-coding transcripts together in parallel. Each transcript is represented by a specific exon or splice junction probe that can identify individual transcripts reliably and accurately. This makes it possible to look beyond the genes and study more subtle and relevant RNA expression changes.This microarray is only available for LncRNA microarray service at Arraystar.
Challenges for LncRNAs Studies
• No comprehensive LncRNAs database is currently available
• Low expression level of LncRNAs
• Difficulties in designing specific LncRNAs probes (LncRNAs often overlap with, or are transcribed antisense to, protein coding genes.)
Highlights:
• Comprehensive and Reliable Array Content: Detects LncRNAs compiled from the most updated transcriptome databases and many other relative literatures
• Most Extensive and Updated Coverage Available: Covers 33,045 LncRNAs and 30,215 protein-coding transcripts
• Specific Exon or Splice Junction Probes: Enables the identification of individual transcripts reliably and accurately
• Efficient and Robust Labeling System: Makes it possible to create Cy3 or Cy5 labeled antisense RNA with low input or degraded RNA samples
• Systematic LncRNA Classification: Helps to identify the putative functional relationship between LncRNAs and their associated protein-coding genes
Data Sources
Specifications:
|
Total Number of Distinct Probes |
60,302 |
|
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 |
Utilizing a random priming method to generate Cy3 or Cy5 labeled antisense RNAs along the entire length of the transcript without 3¡¯ bias |
|
Protein Coding Transcripts (mRNAs) |
30,215 |
|
LncRNAs |
33,045 |
|
LncRNA Sources |
LncRNA collections are based on:
Databases: NCBI Refseq, UCSC Known Gene 5.0 , Ensembl 37.59, H-invDB 7.0, RNAdb 2.0 and NRED;
Literatures: LincRNAs[1], lncRNAs with enhancer-like functions[2], Hox Loci LncRNAs[3], and T-UCRs[4]. |
|
mRNA Sources |
mRNA collection is based on: |
|
Array Format |
8 x 60K |
References:
1. Khalil, A.M., et al., Many human 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.
2. Orom, U.A., et al., Long noncoding RNAs with enhancer-like function in human cells. Cell, 2010. 143(1): p. 46-58.
3. 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.
4. Calin, G.A., et al., Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell, 2007. 12(3): p. 215-29.
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