LncRNA Array Service

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Arraystar LncRNA Arrays are designed to systematically profile lncRNAs along with the entire set of protein-coding mRNAs. They are the best tool for profiling LncRNAs, overcoming many limitations of RNA-seq for lncRNAs often at low abundance.

To incorporate rapid scientific advances and new data, Arraystar has newly released LncRNA Array versions updated to Human V5.0, Mouse V4.0, and Rat V3.0. These new arrays provide the most current, robust, full length LncRNA collections, complete with major upgrades in scientific annotation and analyses.

Benefits

• Most sensitive and best technology for lncRNA profiling, superior to RNA-seq. Learn more>>

• Comprehensive and robust full-length* LncRNA collection curated from the all major latest databases and landmark publications. Learn more>>

• Systematic and specialized lncRNA annotation, including genomic context, epigenomic context*, completeness*, subcellular localization**, miRNA recognition... Learn more>>

• An invaluable tool for LncRNA research with hundreds of high impact publications. Learn more>>

*Applied to Human V5.0   ** Applied to Human V5.0 and Mouse V4.0

Service NameCatalog NoDescriptionFormatPrice
Human V5.0 LncRNA Array Service AS-S-LNC-H 39,317 LncRNAs and 21,174 mRNAs 8*60K
Mouse V4.0 LncRNA Array Service AS-S-LNC-M 37,949 LncRNAs and 22,692 mRNAs 8*60K
Rat V3.0 LncRNA Array Service AS-S-LNC-R 10,333 LncRNAs and 28,287 mRNAs 4*44K

More sensitive and better technology than RNA-seq for lncRNA profiling. 

LncRNAs often express and function at low abundance, buried in other classes of abundant RNAs [1]. There are serious limitations of RNA-seq for lncRNA profiling. 

       •  Poor quantification of lncRNAs due to the low abundance and the lack of completeness in lncRNA annotation
       •  Ambiguous detection of LncRNA isoforms caused by the weak splice profile and the missing connectivity information
       •  Systematic and functional lncRNA annotation database publicly unavailable for RNA seq analysis

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Comprehensive, robust, and most up-to-date LncRNA array contents. 

Unlike protein coding genes, publicly available lncRNAs are often scantily annotated, partial in scope and scattered in collection. Arraystar maintains high quality proprietary lncRNA transcriptome databases that extensively collect lncRNAs through all major public databases and repositories, knowledge-based mining of scientific publications, and our lncRNA discovery pipelines:

Human V5.0: FANTOM5 CAT (v1), GENCODE (v29), RefSeq (Updated to 2018.11), BIGTranscriptome (v1), knownGene (Updated to 2018.11), LncRNAdb, LncRNAWiki, RNAdb, NRED, CLS FL, NONCODE (v5), MiTranscriptome (v2), lncRNA discovery pipeline from more than 47 Tb RNA-seq data. A total of 39,317 lncRNAs in Gold Standard and Reliable LncRNA tiers.  Learn more>>

Mouse V4.0: GENCODE(VM19), RefSeq(Updated to 2018.11), KnownGene(Updated to 2018.11), GenBank.

Rat V3.0: Ensembl (94.rn6), RefSeq(Updated to 2019.01.03).


Systematic lncRNA annotations and analyses incorporating the advances in lncRNA research.

Complete with genomic information, epigenomic context, subclassification, transcript model completeness, subcellular localization, miRNA recognition, conservation, tissue/cell specificity, and small peptide coding potentials, biological process, and disease association, for gaining insights into the complex lncRNA biology.

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Both noncoding lncRNA and protein-coding mRNA expression datasets on the same array to allow their co-expressional and correlational studies.

 

Specifications

Human LncRNA Expression Array V5.0

Total number of distinct probes 60,491
Probe length 60 nt
Probe site mRNA and lncRNA: Specific exon or splice junction sequence along the entire length of transcript.
Probe specificity Transcript-specific
Protein coding mRNAs 21,174
LncRNAs 39,317 (8,393 Gold Standard LncRNAs and 30,924 Reliable LncRNAs)
mRNA sources Refseq, UCSC, GENCODE, FANTOM5 CAT
LncRNA sources Arraystar LncRNA collection pipelines:
lncRNAs from all major databases and literatures up to 2018. “Canonical” or “longest” priority assigned to the transcript for each lncRNA gene.
External Databases (current in 2018):
FANTOM5 CAT (v1), GENCODE (v29), RefSeq (Updated to 2018.11), BIGTranscriptome (v1), knownGene (Updated to 2018.11), LncRNAdb, LncRNAWiki, RNAdb, NRED, CLS FL, NONCODE (v5), MiTranscriptome (v2)
Literatures:
Scientific publications up to 2018
Array Format 8 × 60 K

 

Mouse LncRNA Expression Array V4.0

Total number of distinct probes 60,641
Probe length 60 nt
Probe site mRNA and lncRNA: Specific exon or splice junction sequence along the entire length of transcript.
Probe specificity Transcript-specific
Protein coding mRNAs 22,692
LncRNAs 37,949
mRNA sources Refseq, Known Gene, GENCODE
LncRNA sources Arraystar LncRNA collection pipelines:
lncRNAs from all major databases and literatures up to 2018. “Canonical” or “longest” priority assigned to the transcript for each lncRNA gene.
External Databases (current in 2018):
GENECODE(VM19), RefSeq, KnownGene, GenBank
Literatures:
Scientific publications up to 2018
Array Format 8 × 60 K

 

Rat LncRNA Expression Array V3.0

Total number of distinct probes 38,620
Probe length 60 nt
Probe site mRNA and lncRNA: Specific exon or splice junction sequence along the entire length of transcript.
Probe specificity Transcript-specific
Protein coding mRNAs 28,287
LncRNAs 10,333
mRNA sources Refseq, Ensembl
LncRNA sources Arraystar LncRNA collection pipelines:
lncRNAs from all major databases and literatures up to 2018. “Canonical” or “longest” priority assigned to the transcript for each lncRNA gene.
External Databases (current in 2018):
Refseq, Ensembl
Literatures:
Scientific publications up to 2018
Array Format 4 × 44 K

Arraystar's specially-designed LncRNA Arrays are available only through our LncRNA Array service. We provide full-service LncRNA Array 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 array 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.

Fibrogenic Activity of MECP2 is Regulated by Phosphorylation in Hepatic Stellate Cells. Moran-Salvador E, et al. Gastroenterology, 2019

A long noncoding RNA cluster-based genomic locus maintains proper development and visual function. Wang F,et al. Nucleic Acids Research, 2019

LncRNA PCAT1 activates AKT and NF-kB signaling in castration-resistant prostate cancer by regulating the PHLPP/FKBP51/IKKa complex. Shang Z, et al. Nucleic Acids Research, 2019

Loss of RNA-binding protein GRSF1 activates mTOR to elicit a proinflammatory transcriptional program. Noh J H, et al. Nucleic Acids Research, 2019

NKILA lncRNA promotes tumor immune evasion by sensitizing T cells to activation-induced cell death. Huang D,  et al. Nature immunology, 2018

Long noncoding RNA lnc-TSI inhibits renal fibrogenesis by negatively regulating the TGF-ß/Smad3 pathway. Wang P, et al. Science translational medicine, 2018

GUARDIN is a p53-responsive long non-coding RNA that is essential for genomic stability. Hu W L, et al. Nature Cell Biology, 2018

LncRNA-FEZF1-AS1 promotes tumor proliferation and metastasis in colorectal cancer by regulating PKM2 signaling. Bian Z, et al. Clinical Cancer Research, 2018

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

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

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

Wnt signalling modulates transcribed-ultraconserved regions in hepatobiliary cancers. Carotenuto P,  et al. Gut, 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

The senescence-associated secretory phenotype is potentiated by feedforward regulatory mechanisms involving Zscan4 and TAK1. Zhang B,  et al. Nature communications, 2018

Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA mediated miRNA evasion. Yong-xi Song,et al. Nature communications, 2017

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

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