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Service NameCatalog NoDescriptionFormatPrice
Arraystar Human SE-lncRNA Microarray AS-S-SE-H 7753 SE-lncRNAs and 7040 mRNAs 8*15K
Arraystar Mouse SE-lncRNA Microarray AS-S-SE-M 8222 SE-lncRNAs and 6385 mRNAs 8*15K

Super-enhancer lncRNA (SE-lncRNAs) are a special set of long noncoding RNAs transcribed from super-enhancer genomic loci. SE-lncRNAs play fundamental roles coupled to the active super-enhancers to regulate the gene expression programs that determine the cell lineages and identities. SE-lncRNA have been associated with many human diseases and their expression manifests in profound phenotypic changes [1-3]. Arraystar has developed the first commercially available SE-lncRNA microarrays for human, mouse, and rat to comprehensively, systematically and sensitively profile the SE-lncRNAs and their cis- or trans-regulated coding genes on the same array. The microarray profiling service is provided from RNA sample to analyzed data. The SE-lncRNA profiling is essential to study the super-enhancer activities, mechanisms, functions and diseases.  

References
1. Bradner JE, Hnisz D, Young RA: Transcriptional Addiction in Cancer. Cell 2017, 168(4):629-643.[PMID: 28187285]
2. Alvarez-Dominguez JR, Knoll M, Gromatzky AA, Lodish HF: The Super-Enhancer-Derived alncRNA-EC7/Bloodlinc Potentiates Red Blood Cell Development in trans. Cell Rep 2017, 19(12):2503-2514.[PMID: 28636939]
3. Xiang JF et al: Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res 2014, 24(5):513-531.[PMID: 24662484]
4. Vucicevic D et al: Long ncRNA expression associates with tissue-specific enhancers. Cell Cycle 2015, 14(2):253-260.[PMID: 25607649]
5. Hon CC et al: An atlas of human long non-coding RNAs with accurate 5' ends. Nature 2017, 543(7644):199-204.[PMID: 28241135]
6. Soibam B: Super-lncRNAs: identification of lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation. RNA 2017, 23(11):1729-1742.[PMID: 28839111]

 

Powerful SE-lncRNA collection
• LncRNA foundation using Arraystar premium transcriptome and lncRNA databases for comprehensive, high quality systematic lncRNA compilation.
  - Reliable lncRNAs comprehensively sourced from public databases, such as Refseq, UCSC knownGene, GENCODE, lncRNAdb, RNAdb, NRED and lncRNA Catalogs.
  - Gold standard lncRNAs for well annotated, experimentally studied and Pubmed indexed lncRNAs.
  - Manual curation of lncRNAs from continuous scientific publication review and selection.
• Super-enhancer regions are cataloged in the dbSUPER database.
• SE-lncRNAs are identified by mapping the lncRNAs to the super-enhancer regions.

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Figure 1. Arraystar SE-lncRNA microarray content collection process.

Simultaneous profiling of SE-lncRNAs and their target genes on the same array, to experimentally observe, quantify, correlate and establish accurate regulatory relationships.

SE-lncRNAs transcript isoforms are unambiguously, specifically and reliably detected by unique exon or splice-junction array probes (Fig. 2), with high sensitivity at one transcript per cell.
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Figure 2. The unique sequence of Probe #2’ specifically detects lncRNA CCAT1-L isoform.

Detailed annotation for super-enhancers, SE-lncRNAs and their associated target coding genes.

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Figure 3. A snippet of comprehensive SE-lncRNA annotations. TransID, SE-lncRNA's transcript ID; Gene symbol, SE-lncRNA's gene symbol; Alias, SE-lncRNA's gene symbol alias; Locus, SE-lncRNA's genomic locus(HG19); Subcellular Localization, SE-lncRNA's subcellular localization; Level, SE-lncRNA's annotation in ArrayStar's Human lncRNA microarray; Associated cell or tissue, SE-lncRNA assocaited cell or tissue types from the FANTOM5 CAT annotation; Cancer, experimentally supported associations between lncRNA and human cancer from the database Lnc2Cancer; Disease, experimentally supported lncRNA-disease association from the database LncRNADisease; Super-LncRNA, lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation from Benjamin Soibam et al, 2017; SeqLength; the length of the SE-lncRNA sequence; Sequence, the dna sequence of the SE-lncRNA; Overlapped superenhancer information, information of dbSUPER's super enhancers overlapped with SE-lncRNA; Associated Gene, the ENSEMBL protein-coding genes overlapped with SE-lncRNA or closest to SE-lncRNA; Overlapped Gene symbol, the gene symbol of the genes overlapped with SE-lncRNAs; Overlapped Gene ID, the gene id of the genes overlapped with SE-lncRNAs; Proximal Gene symbol, the gene symbol of the genes closest to SE-lncRNAs; Proximal Gene ID, the gene id of the genes closest to SE-lncRNAs.

Human SE-lncRNA Microarray specifications

Total Number of Distinct Probe 14873
Probe Length 60 nt
Probe Selection Region Probes targeting SE-lncRNA transcript-specific splice junctions or exons
Probe specificity Transcript-specific
Labeling Method An efficient and robust linear amplification method to produce fluorescently labeled target cRNA for sensitive detection of transcripts at even low copy numbers.
SE-lncRNAs & Super-lncRNAs 7753
SE-lncRNA targeted coding genes 7040
SE-lncRNAs sources • Gold standard lncRNAs and reliable lncRNAs from Arraystar Premium transcriptome databases are mapped to the super-enhancer loci catalogued in the dbSUPER database. The lncRNAs overlapped with the super-enhancers are identified and annotated as SE-lncRNAs.
• Enhancer-lncRNAs from literature [4, 5], whose genomic loci overlap with the cataloged super-enhancer loci.
Super-lncRNAs sources Super-lncRNAs are long noncoding RNAs which form RNA:DNA:DNA triplex with multiple anchor DNA sites within the super-enhancers and recruit regulators to the super-enhancers. Super-lncRNAs influence chromatin organization and act as spatial amplifiers for key tissue-specific genes associated with super-enhancers[6].
SE-lncRNA targeted coding genes sources The Refseq genes that either overlap with the SE-lncRNA genomic loci or whose transcription start sites (TSS) fall within 50 kb of the SE-lncRNA genomic loci boundaries are collected as SE-lncRNA targeted coding genes. These genes include 3153 transcription factors (TFs) from TF checkpoint database and 1448 cancer genes from Bushman Lab database.
Array Format 8 * 15K

 

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Figure 1. Human SE-lncRNA Microarray contents.

 

Mouse SE-lncRNA Microarray specifications

Total Number of Distinct Probe 14637
Probe Length 60 nt
Probe Selection Region Probes targeting SE-lncRNA transcript-specific splice junctions or exons
Probe specificity Transcript-specific
Labeling Method An efficient and robust linear amplification method to produce fluorescently labeled target cRNA for sensitive detection of transcripts at even low copy numbers.
SE-lncRNAs 8222
SE-lncRNA targeted coding genes 6385
SE-lncRNAs sources Gold standard lncRNAs and reliable lncRNAs from Arraystar Premium transcriptome databases are mapped to the super-enhancer loci catalogued in the dbSUPER database. The lncRNAs overlapped with the super-enhancers are identified and annotated as SE-lncRNAs.
SE-lncRNA targeted coding genes sources The Refseq genes that either overlap with the SE-lncRNA genomic loci or whose transcription start sites (TSS) fall within 50 kb of the SE-lncRNA genomic loci boundaries are collected as SE-lncRNA targeted coding genes. These genes include 2883 transcription factors (TFs) from TF checkpoint database and 593 cancer genes from SBCDDB database.
Array Format 8 * 15K

 

SE-lncRNA-database-mouse
Figure 2. Mouse SE-lncRNA Microarray contents.

Arraystar's specially-designed SE-LncRNA microarrays are available only through our SE-LncRNA microarray service. We provide full-service SE-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

Efficient labeling method to achieve high sensitivity and high accuracy of SE-lncRNA quantification
Super-enhancer lncRNAs are generally labile and short in half-lives. They can function at low copy numbers per cell to activate the target genes by cis-mechanism. For example, LncRNA-HOTTIP can activate the HOXA gene cluster with an average of less than one copy per cell. 

To accurately detect and quantify the transient, low level SE-lncRNAs, Arraystar scientists have developed an efficient and robust linear amplification method to generate ample fluorophore-labeled cRNA for both polyadenylated and non-polyadenylated transcripts. In this method, an optimized mixture of oligo(dT) and random primers, each containing a T7 polymerase promoter, is annealed to the RNA. The cDNA is synthesized by reverse transcription followed by 5’ adapter annealing and PCR amplification. Finally, cyanine 3- or cyanine 5-labeled cRNA is synthesized by in vitro transcription from the T7 promoter by T7 RNA polymerase (Figure 1).

The labeling procedure greatly increases the cRNA yield from low-abundance or degraded RNA molecules by more than 100-fold over conventional methods.

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Figure 1. Arraystar’s cRNA Labeling Procedure. (1) First strand cDNA synthesis and 5’ adapter annealing. RNA is primed by a mixture of oligo(dT) and random primers containing a T7 polymerase promoter and reverse transcribed into first strand cDNA. 5’-adapter is annealed to the 3’-end of the first strand cDNA during the reverse transcription. (2) PCR amplification. Double strand cDNA is amplified using the RT primer and 5’-Adapter sequences by low cycles of PCR. (3) In vitro transcription and labeling of antisense RNA (aRNA). Fluorescently labeled antisense RNAs are synthesized by in vitro T7 polymerase transcription from the T7 promoter using a Cy3- or Cy5-nucleotide substrate. The linear amplification reserves the native transcript levels and copies along the entire length of the transcript without 3’ bias.