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LncRNA Research

Long Non-Coding RNA Profiling Challenges and Solutions

 

LncRNAs are RNA transcripts that resemble protein-coding messenger RNAs (mRNAs) in practically every way except that they do not encode proteins. LncRNAs have recently emerged as major players in governing fundamental biological processes. Profiling expression levels of LncRNAs poses a number of special challenges, including:

 Lack of comprehensive and reliable public LncRNA databases

 Low expression levels of LncRNAs

• Overlap of many LncRNAs with protein-coding mRNAs

Lack of comprehensive and reliable public LncRNA databases

Despite increasing attention paid to LncRNAs in recent years, there has been no single, comprehensive, or reliable public database of all the known LncRNAs in humans, mice, rats, or other organisms.  LncRNAs are instead curated among several disparate public databases, such as RefSeq and Ensembl. To make matters further difficult, there are thousands of additional LncRNAs that are only described in publications.

One unified, reliable LncRNA database: The Arraystar LncRNA Arrays for human, mouse, and rat are carefully constructed from well-known public databases and landmark publications, using a stringent computational filtering protocol. Learn more.

Low Expression Levels of LncRNAs

LncRNAs tend to be expressed at much lower levels than mRNAs. This phenomenon makes profiling LncRNA expression by next-generation sequencing (NGS) difficult-many more NGS reads are required to achieve adequate coverage of LncRNAs compared with mRNAs.  Typically, 30 million pass-filter reads using Illumina NGS technology provide sufficient coverage for mRNAs. By contrast, 180 million to 200 million Illumina reads are needed for adequate coverage of LncRNAs.

Comprehensive LncRNA coverage at a fraction of the cost of NGS: Arraystar LncRNA arrays provide comprehensive coverage of LncRNAs and mRNAs in humans, mice, and rats. Therefore, you can use proven, cost-effective microarray technology to provide sufficient coverage of both LncRNAs and mRNAs-all on a single chip! Learn more.

Overlap of LncRNAs with mRNAs

Many LncRNAs overlap with mRNAs on either the sense or antisense strand, making it difficult to distinguish between the two classes of transcripts.

Transcript-specific probe design: Unlike most companies, who target their gene-specific microarray probes to the 3' end of the transcript, Arraystar targets their probes to exons and splice junctions. These transcript-specific probes give you the ability to distinguish between multiple transcript isoforms, as well as between LncRNAs and overlapping mRNAs. Learn more.

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Publications >>

Epitranscriptomic Array
Xiong Y W, et al. (2024) Nature Communications

[PMID: 38355624] 

tRNA Sequencing
Wu X, et al. (2024) Nature Cancer 

[PMID: 38519786]

Circular RNA Array
Zhong GL, et al. (2023) Molecular Cancer 

[PMID: 37004067] 

 

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Non-coding RNA and Epitranscriptomic Solutions
• Circular RNA Microarrays
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