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Service NameCatalog NoDescriptionFormatPrice
Human LncRNA Array Service AS-S-LNC-H 20,730 mRNAs and 40,173 LncRNAs 8*60K
Mouse LncRNA Array Service AS-S-LNC-M 24,881 mRNAs and 35,923 LncRNAs 8*60K
Rat LncRNA Array Service AS-S-LNC-R 24,626 mRNAs and 13,611 lncRNAs 4*44K

Arraystar scientists have developed a full range of powerful microarrays for evaluating the global expression levels of LncRNAs in humans, mice, and rats. In 2009, we launched the Arraystar LncRNA Microarray V1.0 - the first commercial microarray for expression profiling of LncRNAs and mRNAs side by side. This ground-breaking microarray made us the industry leader in LncRNA research. Following the popularity of this innovative scientific tool, the Arraystar LncRNA Microarray V2.0 was released in March 2011, quickly becoming our best-selling product and contributing greatly to driving the heightened interest in this intriguing group of non-coding RNAs.

To date, these powerful microarrays have proven themselves to be an invaluable resource in LncRNA research touting many high impact publications. To incorporate rapid scientific advances and new data, Arraystar released our version 4.0 Human , version 3.0 Mouse and version 2.0 Rat LncRNA Expression Microarray in succession, which provide a newly-updated and stringent LncRNA collection, as well as additional non-coding RNAs of interest. In addition, the Arraystar Human LncRNA Microarray V4.0 features an enhancement of our concise and scientific LncRNA subgroup and classification.

Arraystar LncRNA Microarrays, with transcript-specific detection for accurate detection of multiple transcript isoforms, are the most sensitive and best technology to profile lncRNA expression, better than RNA-seq for lncRNA profiling as lncRNAs are often at lower abundance.Because,

1) For mere detection of the presence of an lncRNA, a few reproducible counts unique to that lncRNA are required.
2) But for quantification, at least hundreds read counts are required. LncRNAs as a population are ~10x less than mRNA. Count numbers at these levels are not nearly sufficient for differential expression analysis.
3) Many lncRNAs have complex overlapping relationship with mRNA genes, sequencing reads from an lncRNA are not necessarily unique to the lncRNA, which demands deep sequencing reads to construct transcripts for novel lncRNA discovery.
In short, a large proportion of lncRNAs are not sufficiently quantifiable by RNA-seq at regular sequencing depth. Deep, paired-end, strand-directional sequencing is required for quantification and novel lncRNA discovery.

Human LncRNA Microarray V4.0
• Gold-Standard LncRNAs, Reliable LncRNAs and mRNAs certified with proteins on the same chip.

Unlike protein coding genes, publically available lncRNAs are often scantily annotated,partial in scope and scattered in collection. Arraystar maintains high quality proprietary transcriptome and lncRNA databases to extensively collect lncRNAs through our lncRNA discovery pipelines, external data sources, and knowledge-based mining of scientific publications. Arraystar Human LncRNA Microarray V4.0 has a total of 40,173 lncRNAs in two major lncRNA collections, 7,506 for Gold Standard LncRNAs and 32,667 Reliable LncRNAs, from more than 47 Tb worth of RNA-seq data and all major public databases and repositories, such as Refseq, USCS Known Genes, GENCODE, lincRNA catalogs, lncRNAdb, T-UCRs, RNAdb, NRED, and scientific publications. Learn more>

• Systematic and functional lncRNA annotations and analyses to incorporate advances in lncRNA research and are complete with genomic information, subclassification, and potential regulatory mechanisms, to gain insights into the complex lncRNA biology. LncRNAs associated with biological processes or human diseases are annotated and referenced. Learn more>
• A wealth of information for co-expressional and correlational studies of non-coding regulatory lncRNAs with protein coding mRNAs. Learn more>


Mouse and Rat LncRNA Microarray
• LncRNAs are comprehensively collected from the most updated public transcriptome databases, including RefSeq [1], Ensembl [2],lncRNAdb [3], and landmark publications [4-8].
• LncRNAs from the databases and publications are filtered using a stringent computational pipeline for greater reliability. Learn more>
• LncRNAs are classified 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. Learn more>

Data Sources

Human Database: Composition of the Arraystar Human LncRNA Expression Microarray V4.0

Mouse Database: Composition of the Arraystar Mouse LncRNA Expression Microarray V3.0

Rat Database: Composition of the Arraystar Rat LncRNA Expression Microarray V2.0


Specifications

Human LncRNA Expression Microarray V4.0

Total number of distinct probes 60,903
Probe selection region Specific exon or splice junction along the entire length of the transcript
Probe specificity Transcript-specific
Labeling method cRNAs are labeled along the entire length without 3’ bias, even for degraded RNA at low amount.
Total LncRNAs 40,173
Gold Standard LncRNAs 7,506
Reliable LncRNAs 32,667
Transcribed pseudogenes 699
Protein coding mRNAs 20,730
LncRNA sources Databases current in 2015:
Refseq, UCSC, GENCODE, LncRNAdb, RNAdb, NRED, lincRNA catalogs (Cabili et al 2011, Clark et al 2015, Iyer et al 2015), ENCODE CAGE Clusters, PolyA-seq, deep RNA-Seq and capture seq data repositories.
 Arraystar LncRNA collection pipelines. Literature:
Scientific publications up to 2015.
mRNA sources  Refseq, GENCODE in conjunction with UniProt

Rererence
 

Mouse LncRNA Expression Microarray 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;
Literature:
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

Reference
 

Rat LncRNA Expression Microarray V2.0

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

Arraystar's specially-designed LncRNA microarrays are available only through our LncRNA microarray service. We provide full-service LncRNA microarray profiling, from sample preparation to in-depth data analysis. Our step-by-step quality controls are designed to ensure you get the most reliable results. Just send us your samples, and we'll do the rest!

Please refer to Sample Submission for details in how to get your project started.

•  RNA isolation (Optional)

•  RNA QC

•  cDNA synthesis

•  Target preparation by labeling with Cy3

•  Array hybridization, washing, and scanning

•  Data extraction, analysis and summarization

Arraystar's experienced scientists have intimate knowledge of the LncRNA microarray platform and are experts in the analysis and interpretation of LncRNA profiling data. This familiarity enables us to employ the most robust methods for normalization and data analysis including subgroup classification.

2 Fold Up/Down-regulated LncRNAs Pass t-test (Group 1 vs. Group 2 )
  P-value, Fold Change and Regulation Annotation
Probe Name P-value
<0.05
FC Absolute>2 Regulation LncRNA_level Genbank Accession Gene Symbol Source Relationship
ASHGV40057870 0.0012 4.1664 Up  Gold NR_003716 HOTAIR Refseq Intergenic
ASHGV40057755 0.0236 2.6177 Up  Gold NR_023920 WT1AS Refseq Bidirection
ASHGV40010435 0.0001 2.5284 Down Reliable ENST00000548740 RP11-510I5.4 GENCODE Intergenic
ASHGV40045180 0.0018 3.0126 Down Reliable ENST00000508884 RP1-27K12.4 GENCODE natural antisense

Table 1.  Differentially expressed LncRNAs screening. Differentially expressed LncRNAs (Fold change>2, p-value<0.05) in Group1 vs Group2. In column "Regulation", "Up" indicates up-regulated, "Down" indicates down-regulated.

Deep data mining and advanced analyses (Fig. 1 and 2, for example) are available to carry you further with the wealth of information generated by the microarrays.

CNC

Figure 1. Coding-noncoding interaction Co-expression (CNC) subnetwork of an lncRNA-HEIH in hepatocellular carcinoma.

 

LncRNA_GSEA

Figure 2. Lnc-GSET to identify enrichment of lncRNAs in biological functions.

The LINK-A lncRNA interacts with PtdIns (3, 4, 5) P3 to hyperactivate AKT and confer resistance to AKT inhibitors. Lin A, et al. Nature Cell Biology, 2017  

A novel lncRNA GClnc1 promotes gastric carcinogenesis and may act as a modular scaffold of WDR5 and KAT2A complexes to specify the histone modification pattern. Sun T T, et al. Cancer discovery, 2016

Integrative Transcriptome Analyses of Metabolic Responses in Mice Define Pivotal LncRNA Metabolic Regulators.Yang L, et al.  Cell Metabolism, 2016.

Differential transcriptome expression in human nucleus accumbens as a function of loneliness. Canli T, et al. Molecular Psychiatry?, 2016

Long noncoding RNA Tug1 regulates mitochondrial bioenergetics in diabetic nephropathy. Long J, et al. The Journal of Clinical Investigation, 2016

Long Non-coding RNA DILC Represses Self-renewal of Liver Cancer Stem Cells via Inhibiting Autocrine IL-6/STAT3 Axis. X Wang, et al. Journal of Hepatology, 2016

An acetyl-L-carnitine switch on mitochondrial dysfunction and rescue in the metabolomics study on aluminum oxide nanoparticles.Li X, et al.Particle and Fibre Toxicology, 2016

Long non-coding RNA LINC00092 acts in cancer-associated fibroblasts to drive glycolysis and progression of ovarian cancer. Zhao L, et al. Cancer Research, 2017

Integrative Functional Transcriptomic Analyses Implicate Specific Molecular Pathways in pulmonary toxicity from Exposure to Aluminum Oxide Nanoparticles. Li X, et al.Nanotoxicology,2016

A novel lncRNA uc. 134 represses hepatocellular carcinoma progression by inhibiting CUL4A-mediated ubiquitination of LATS1.Ni W,et al.Journal of Hematology & Oncology, 2017

Circulating “lncRNA OTTHUMT00000387022” from Monocytes as a Novel Biomarker for Coronary Artery Disease. Yue Cai, et al. Cardiovascular Research, 2016

DC-SIGNR by influencing the lncRNA HNRNPKP2 upregulates the expression of CXCR4 in gastric cancer liver metastasis. Zhang Y, et al. Molecular Cancer, 2017

LncRNAs expression profiling in normal ovary, benign ovarian cyst and malignant epithelial ovarian cancer. Wang H,  et al. Scientific Reports, 2016

LncRNA-N1LR Enhances Neuroprotection Against Ischemic Stroke Probably by Inhibiting p53 Phosphorylation. Wu Z, et al. Molecular Neurobiology, 2016

Microarray Analysis of lncRNA and mRNA Expression Profiles in Patients with Neuromyelitis Optica. Xu J, et al. Molecular Neurobiology, 2016

Long noncoding RNA related to periodontitis interacts with miR-182 to upregulate osteogenic differentiation in periodontal mesenchymal stem cells of periodontitis patients. Wang L, et al. Cell Death & Disease, 2016.

Comprehensive analysis of differentially expressed profiles of lncRNAs and circRNAs with associated co-expression and ceRNA networks in bladder carcinoma.Mengge Huang, et al.Oncotarget,2016

Selected Publications>>

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