Circular RNA Array Service

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Arraystar Circular RNA Arrays, systematically profiling the expression of circular RNAs, are the only commercially available tool to most effectively profile, analyze and explore this new and exciting world of noncoding RNAs. We offer the specialized Circular RNA array service, from sample to publishable data!

Benefits

• Comprehensive collection of SE-lncRNAs and super-lncRNAs >>
• Simultaneous profiling of the target mRNA genes associated with SE-lncRNAs >>
• Entire sets of transcription factors and oncogenes >>
• Detailed annotations for SE-lncRNA, super-enhancer, and targets >>
• Unambiguous and reliable SE-lncRNA isoform detection >>
• Efficient target labeling for sensitive detection of labile SE-lncRNAs >>
• Superior quantification of LncRNAs over RNA-seq >>

 

Service NameCatalog NoDescriptionFormatPrice
Arraystar Human Circular RNA Array AS-S-CR-H-V2.0 13,617 circular RNAs 8*15K
Arraystar Mouse Circular RNA Array AS-S-CR-M-2.0 14,236 circular RNAs 8*15K
Arraystar Rat Circular RNA Array AS-S-CR-R-V2.0 14,145 circular RNAs 8*15K

• Specific Circular Junction Probes

Reliably and accurately identify individual circRNAs, even in the presence of their linear counterparts (Fig. 1).

circRNA2

Figure 1. Arraystar circRNA Array V2.0 uses specific circular junction probes to accurately and reliably detect each individual circRNAs, even in the presence of their linear counterparts. The linear RNA at the bottom is alternatively processed to generate a circular variant above. A probe is designed to target the circRNA-specific junction site, where the 5' end of exon A joins together with the 3' end of exon B.

• Detailed annotation for circRNA-miRNA association

Annotation of potential miRNA target sites on the circular RNAs helps to unravel their functional roles as a natural miRNA sponge (Fig. 2).

circRNA3

Figure 2. The association between circular RNA and conserved miRNAs is annotated in detail.

• The preferred choice over RNA-sequencing, as RNA-seq is currently inadequate for such task due to the particular properties of circular RNA.    Learn more >

1) Circular junction read counts are only a fraction of the circular RNA. They are much lower than the linear RNA at the same abundance level.

2) For detection of the circular RNA presence, a few reproducible counts are required. But for quantification, at least hundreds of read counts are required.

3) Even with combined large datasets and studies, most of the known circular RNAs have just a few read counts. Count numbers at these levels are not nearly sufficient for differential expression analysis.
In short, circular RNA sequencing can be used for novel discovery by a few read counts, but is inadequate for differential expression analysis even at modest abundance levels.

6

Figure 3. RNA-seq quantification reliability vs read depth. Typical RNA-seq has a depth of < 30 mil reads for mRNAs (blue circle), which is  < 0.5 mil for cross circular junction reads (red circle). Less than 5% circular junctions can be reliably quantified. Adopted from Labaj et al, (2011) Bioinformatics [PMID 21685096].

• Spike-in RNA controls

A set of exogenous RNA controls developed by the External RNA Controls Consortium (ERCC) are added to the RNA samples. With the spike-in controls, procedural effects occurring during RNA amplification, labeling, and hybridization can be corrected. The limit of detection is more accurately determined, and the results across samples are compared more reliably.

• Guaranteed performance

- Better sensitivity: Low abundance RNAs are accurately detected with a wide dynamic range of over 5 orders of magnitude (Fig. 4).

circRNA4

Figure 4. A wide dynamic detection range of over 5 orders of magnitude with Arraystar's circRNA Arrays.

- High Reproducibility: Technical replicates show tight correlation on Arraystar circRNA Arrays (R2>0.9)  (Fig. 5).

circRNA5

Figure 5.   High reproducibility on Arraystar circRNA arrays.

Circular RNA (circRNA) is a novel type of RNA that, unlike linear RNA, forms a covalently closed continuous loop, some of which are highly represented in the eukaryotic transcriptome. Most of these circRNAs are generated from exonic or intronic sequences, are conserved across species, and often show tissue/developmental-stage-specific expression. Circular RNAs are more stable than linear RNAs owing to their higher nuclease stability, which constitutes an enormous advantage from a clinical point of view as a novel class of biomarkers. In addition, circRNAs have been shown to function as natural miRNA sponge transcripts, the so-called competing endogenous RNAs (ceRNAs) in diverse species. Their interaction with disease associated miRNAs suggests the potential importance of circular RNAs in disease regulation.

To facilitate the analysis of circRNAs, Arraystar has developed the first commercially-available circRNA arrays for human , mouse and rat. In order to detect circRNAs comprehensively and reliably, we have updated the circRNA repertoire represented in the previous Version 1.0 and launched the newly designed V2.0.

It is the only practical platform for highly sensitive and specific circular RNA profiling available for biologists with a complete from RNA sample to publishable data service. To learn more about the publications by our clients, click here.

Human Database

Total Number of Distinct Probes 13,617
Probe Length 60 nt
Probe Selection Region Probes targeting circRNA-specific junctions
Probe Specificity Transcript-specific
Labeling Method Random primer labeling coupled with RNase R sample pretreatment to ensure specific and efficient labeling of circular RNAs.
Circular RNA Sources
Salzman's circRNAs [4] 8,529
Memczak's circRNAs [3] 1,601
Zhang's circRNAs [6] 93
Zhang's circRNAs [5] 4,980
Jeck's circRNAs [2] 3,769
Guo's circRNAs [1] 5,536
Array Format 8 * 15K

 

 

 

 

 

 

 

 

 

 

 

Mouse Database

Total Number of Distinct Probes 14,236
Probe Length 60 nt
Probe Selection Region Probes targeting circRNA-specific junctions
Probe Specificity Transcript-specific
Labeling Method Random primer labeling coupled with RNase R sample pretreatment to ensure specific and efficient labeling of circular RNAs.
CircRNA Sources
Memczak's circRNAs 1,750
Guo's circRNAs 570
You's circRNAs 13,300
Array Format 8 * 15K
 

Rat Database

Total Number of Distinct Probes 14,145
Probe Length 60 nt
Probe Selection Region Probes targeting circRNA-specific junctions
Probe Specificity Transcript-specific
Labeling Method Random primer labeling coupled with RNase R sample pretreatment to ensure specific and efficient labeling of circular RNAs.
CircRNA Sources
You Xintian's circRNAs [7] 12,298
Mouse circRNA orthologs 1,668
Human circRNA orthologs 179
Array Format 8 * 15K


References1. Guo, J. U., V. Agarwal, et al. (2014). "Expanded identification and characterization of mammalian circular RNAs." Genome Biol 15(7): 409.
2. Jeck, W. R., J. A. Sorrentino, et al. (2013). "Circular RNAs are abundant, conserved, and associated with ALU repeats." RNA 19(2): 141-157.
3. Memczak, S., M. Jens, et al. (2013). "Circular RNAs are a large class of animal RNAs with regulatory potency." Nature 495(7441): 333-338.
4. Salzman, J., R. E. Chen, et al. (2013). "Cell-type specific features of circular RNA expression." PLoS Genet 9(9): e1003777.
5. Zhang, X. O., H. B. Wang, et al. (2014). "Complementary sequence-mediated exon circularization." Cell 159(1): 134-147.
6. Zhang, Y., X. O. Zhang, et al. (2013). "Circular intronic long noncoding RNAs." Mol Cell 51(6): 792-806.7. You X., I. Vlatkovic, et al. (2015). "Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity." Nat Neurosci 18(4): 603-610. .

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

• RNA isolation (optional)
• RNA QC
• Determine the purity and concentration of total RNA
• Assess the integrity of total RNA
• RNase R treatment
• cDNA synthesis
• Labeling
• Array hybridization, washing, and scanning
• Data extraction, analysis and summarization
• Streamlined and optimized labeling pipeline

Figure 1. A random primer-based labeling system is coupled with RNase R-based sample pretreatment to efficiently remove linear RNAs, and specifically label circular RNAs.

• Spike in RNA controls
Adds a set of exogenous RNA controls developed by the External RNA Controls Consortium (ERCC) to RNA samples.

With these spike-in controls, procedural effects occurring during RNA amplification, labeling, and hybridization can be corrected. The limit of detection is more accurately determined, and the results across samples are compared more reliably.

                                                                                                                                                                                                                   

Detailed annotation for circRNA-miRNA association
Annotates the circRNAs with the potential target sites of miRNAs, which will be helpful for unraveling their functional roles as a natural miRNA sponge.

CircRNA_2
Figure 1. The circular RNA and its asscociated conserved miRNAs are annotated in detail.

Differentially Expressed circRNAs
Differentially expression circRNAs are selected by the magnitude of change and the statistic significance in p-value, which are visualized on Volcano plots. The expression patterns are displayed on hierarchical clustering heatmaps.

CircRNA_3
Figure 2. Differentially expressed circRNAs, the binding with multiple microRNAs, and the details of the microRNA Response Elements (MREs).

A Circular RNA Protects Dormant Hematopoietic Stem Cells from DNA Sensor cGAS-Mediated Exhaustion. Xia P, et al. Immunity, 2018

circEPSTI1 as a prognostic marker and mediator of triple-negative breast cancer progression. Chen B, et al. Theranostics, 2018

Circular RNA MTO1 acts as the sponge of miR-9 to suppress hepatocellular carcinoma progression. Han D, et al. Hepatology (Baltimore, Md.), 2017 

A Circular RNA Binds To and Activates AKT Phosphorylation and Nuclear Localization Reducing Apoptosis and Enhancing Cardiac Repair. Zeng Y, et al. Theranostics, 2017

circRNA Mediates Silica-Induced Macrophage Activation Via HECTD1/ZC3H12A-Dependent Ubiquitination. Zhou Z, et al. Theranostics, 2017

The circular RNA circPRKCI promotes tumor growth in lung adenocarcinoma. Qiu M, et al. Cancer Research, 2018

Enhanced breast cancer progression by mutant p53 is inhibited by the circular RNA circ-Ccnb1. Fang L,et al. Cell Death & Differentiation, 2018

circRNA_100290 plays a role in oral cancer by functioning as a sponge of the miR-29 family. Chen L, et al. Oncogene, 2017

CircIRAK3 sponges miR-3607 to facilitate breast cancer metastasis. Wu J, et al. Cancer Letters, 2018

Tumor-released exosomal circular RNA PDE8A promotes invasive growth via the miR-338/MACC1/MET pathway in pancreatic cancer. Li Z, et al. Cancer letters, 2018

Silencing circular RNA hsa_circ_0000977 suppresses pancreatic ductal adenocarcinoma progression by stimulating miR-874-3p and inhibiting PLK1 expression. Huang W J, et al. Cancer Letters, 2018   

Circular RNA_LARP4 inhibits cell proliferation and invasion of gastric cancer by sponging miR-424-5p and regulating LATS1 expression. Zhang J, et al. Molecular Cancer, 2017   

RNA-binding Protein Trinucleotide repeat-containing 6A Regulates the Formation of Circular RNA 0006916, with Important Functions in Lung Cancer Cells. Dai X, et al. Carcinogenesis, 2018

CircRNA-0004904, CircRNA-0001855, and PAPP-A: Potential Novel Biomarkers for the Prediction of Preeclampsia. Jiang M, et al. Cellular Physiology and Biochemistry, 2018

Hsa_Circ_0001275: A Potential Novel Diagnostic Biomarker for Postmenopausal Osteoporosis. Zhao K, et al. Cellular Physiology and Biochemistry, 2018

Expression Profiling of Circular RNAs and Micrornas in Heart Tissue of Mice with Alcoholic Cardiomyopathy. Yang Y, et al. Cellular Physiology and Biochemistry, 2018

More publications in 2018>>

More publications in 2017>>

More publications in 2016>>