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

• The only practical platform for highly sensitive and specific circular RNA profiling. Learn more>>
• Circular junction-specific probes, linear RNA removal and efficient circRNA labeling ensure the most specific, accurate and reliable circRNA expression profiling.
• Detailed annotation specific to circRNA biology, e.g. miRNA binding sites, miRSVR scores and conservation status, to unravel functional roles as miRNA sponges.
• The preferred choice over RNA-sequencing, due to the particular properties of circular RNA.  Learn more>

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].

• 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

Circular RNA Array Service

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.

                                                                                                                                                                                                                  

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).

AUF1 ligand circPCNX reduces cell proliferation by competing with p21 mRNA to increase p21 production. Tsitsipatis D, et al. Nucleic Acids Research, 2021

Targeting Mitochondria-Located circRNA SCAR Alleviates NASH via Reducing mROS Output. Qiyi Zhao, et al. Cell, 2020

Extracellular Vesicle-Mediated Delivery of CircSCMH1 Promotes Functional Recovery in Rodent and Nonhuman Primate Ischemic Stroke Models. Yang L, et al. Circulation, 2020

1972P Circular RNA is associated with enz***amide resistant prostate cancer. Lim M C J, et al. Annals of Oncology, 2020

Circular RNAs as biomarkers in liquid biopsy in colorectal cancer. Valladares-Ayerbes M, et al. Journal of Clinical Oncology, 2020

A psychiatric disease-related circular RNA controls synaptic gene expression and cognition. Zimmerman A J, et al. Molecular Psychiatry, 2020

CircPTK2 (hsa_circ_0005273) as a novel therapeutic target for metastatic colorectal cancer. Yang H, et al. Molecular Cancer, 2020

Circ-AKT3 inhibits clear cell renal cell carcinoma metastasis via altering miR-296-3p/E-cadherin signals. Xue D, et al. Molecular Cancer, 2019

circGSK3ß promotes metastasis in esophageal squamous cell carcinoma by augmenting ß-catenin signaling. Hu X, et al. Molecular Cancer, 2019

A Noncoding Regulatory RNAs Network Driven by Circ-CDYL Acts Specifically in the Early Stages Hepatocellular Carcinoma. Wei Y, et al. Hepatology, 2019

Circular RNA CircFndc3b modulates cardiac repair after myocardial infarction via FUS/VEGF-A axis. Garikipati V., et al. Nature Communications, 2019

FOXP1 circular RNA sustains mesenchymal stem cell identity via microRNA inhibition. Cherubini A, et al. Nucleic Acids Research, 2019

Circular RNA cESRP1 sensitises small cell lung cancer cells to chemotherapy by sponging miR-93-5p to inhibit TGF-ß signalling. Huang W, et al. Cell Death & Differentiation, 2019

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

PRMT5 circular RNA promotes metastasis of urothelial carcinoma of the bladder through sponging miR-30c to induce epithelial-mesenchymal transition. Chen X, et al. Clinical Cancer Research, 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

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