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

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 microarrays 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.

• The only practical platform for highly sensitive and specific circular RNA profiling available for biologists as full RNA sample to data service.
• Circular junction-specific probes, linear RNA removal by RNase R treatment and efficient circRNA labeling ensure the most specific, accurate and reliable circRNA expression profiling, even in the predominant presence of linear RNAs.
• 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, as RNA-seq is currently inadequate for such task due to the particular properties of circular RNA. Because:

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. Learn more>

We provide full-service circular RNA 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!

• 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 Microarray 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 microarrays.

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

circRNA5

Figure 5.   High reproducibility on Arraystar circRNA arrays.

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).

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

Changing expression profiles of lncRNAs, mRNAs, circRNAs and miRNAs during osteoclastogenesis. Dou C, et al. Scientific Reports, 2016

Circular RNA Related to the Chondrocyte ECM Regulates MMP13 Expression by Functioning as a MiR-136 'Sponge' in Human Cartilage Degradation. Liu Q, et al. Scientific Reports, 2016

CircRNA_000203 enhances the expression of fibrosis-associated genes by derepressing targets of miR-26b-5p, Col1a2 and CTGF, in cardiac fibroblasts. Tang C M,  et al.Scientific Reports, 2017

Circ100284, via miR-217 regulation of EZH2, is involved in the arsenite-accelerated cell cycle of human keratinocytes in carcinogenesis. Xue J,  et al. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 2017

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

CircRNA expression pattern and circRNA-miRNA-mRNA network in the pathogenesis of nonalcoholic steatohepatitis. Jin X  et al. Oncotarget,2016

Microarray Expression Profile of Circular RNAs in Heart Tissue of Mice with Myocardial Infarction-Induced Heart Failure. Wu H J, et al. Cellular Physiology and Biochemistry, 2016

Potential Significance of Circular RNA in Human Placental Tissue for Patients with Preeclampsia. Qian Y,  et al.Cellular Physiology and Biochemistry, 2016

Circular RNA Expression Profile of Pancreatic Ductal Adenocarcinoma Revealed by Microarray. Li H, et al. Cellular Physiology and Biochemistry, 2016

Circular RNA expression in basal cell carcinoma.Sand M et al.Epigenomics,2016

Circular RNA expression in cutaneous squamous cell carcinoma.Sand M et al.Journal of Dermatological science,2016

Characterization of hsa_circ_0004277 as a New Biomarker for Acute Myeloid Leukemia via Circular RNA Profile and Bioinformatics Analysis. Li W, et al. International Journal of Molecular Sciences, 2017

Microarray profiling of circular RNAs in human papillary thyroid carcinoma. Peng N, et al. PloS one, 2017

Identification of differentially expressed circular RNAs in human colorectal cancer. Zhang P, et al. Tumor Biology, 2017      

Profiling and bioinformatics analyses reveal differential circular RNA expression in radioresistant esophageal cancer cells. Su H, et al. Journal of Translational Medicine, 2016.

A novel identified circular RNA, circRNA_010567, promotes myocardial fibrosis via suppressing miR-141 by targeting TGF-ß1. Zhou B, Xu H Y. Biochemical and Biophysical Research Communications, 2017     

Circular RNA expression alterations are involved in OGD/R-induced neuron injury. Lin SP, et al.Biochemical and Biophysical Research Communications, 2016

Comprehensive circular RNA profiling reveals that circular RNA100783 is involved in chronic CD28-associated CD8( )T cell ageing. Wang YH, et al. Immunity & Ageing, 2015

Circular RNA in blood corpuscles combined with plasma protein factor for early prediction of pre-eclampsia. Zhang YG et al. BJOG.  2016

Microarray analysis of circular RNA expression patterns in polarized macrophages. Zhang Y, et al. International journal of molecular medicine, 2017

Circular BANP, an upregulated circular RNA that modulates cell proliferation in colorectal cancer. Zhu M,  et al. Biomedicine & Pharmacotherapy, 2017

Circular RNA: a novel biomarker for progressive laryngeal cancer. Xuan L et al. American Journal of Translational Research?, 2016

Circular RNA and gene expression profiles in gastric cancer based on microarray chip technology. W Sui, et al.Oncology Reports,2017

Circular RNA expression alterations are involved in OGD/R-induced neuron injury.  Lin SP et al. Biochemical and Biophysical Research Communications?, 2016

hsa_circRNA_103636: potential novel diagnostic and therapeutic biomarker in Major depressive disorder. Cui X, et al. Biomarkers in Medicine?, 2016

Comprehensive Circular RNA Profiling Reveals That hsa_circ_0005075, a New Circular RNA Biomarker, Is Involved in Hepatocellular Crcinoma Development.Shang, Xingchen et al.Medicine,2016

Comprehensive analysis of circRNA expression patterns in small hepatocellular carcinoma by integrating circRNA and gene expression data. Ou M, et al. Int J Clin Exp Med, 2017

Noncoding RNAs in human intervertebral disc degeneration: An integrated microarray study. Liu X, et al. Genomics Data, 2015

Microarray expression profile of circular RNAs in human pancreatic ductal adenocarcinoma. Qu S, et al. Genomics Data, 2015