circRNA-Seq

Recent years there has been a considerable increase in interest in circRNA studies, especially circRNA expression analysis. CD Genomics provides circRNA sequencing (circRNA-seq) service for identifying circRNAs, quantifying circRNA expression levels, and characterizing their potential functions. Please contact our expert team to discuss how our circRNA-seq service can refine your NGS projects.

Overview

Circular RNAs (circRNAs) are a large class of naturally occurring endogenous non-coding RNAs (ncRNAs) that contain a covalent circular structure formed by back-splicing without a 3' tail and or 5' cap. Previous studies have shown that circRNAs are widely present in a relatively low abundance compared with linear mRNA molecules and some are conserved in eukaryotic organisms. Although the function of most circRNAs is still ambiguous, studies have revealed that circRNAs function as molecular sponges to sequester specific microRNAs (miRNAs) repress their endogenous activity. Studies also highlighted the critical roles of circRNAs in cellular metabolic processes and cancer occurrence and progression. Thus, circRNA expression analyses help interpret molecular fundamentals of complex traits and diseases. RNA sequencing (RNA-seq) has emerged as a transcriptome-wide method to characterize and quantify circRNAs. A number of computational approaches have been developed for extracting, characterizing, and quantifying circRNAs. Dissection of changes in circRNA expression among different samples is a routine analysis in circRNA studies to evaluate the significance of differentially expressed circRNAs. CD Genomics offers circRNA-seq to investigate miRNA sponges and the regulatory function in gene expression.

Features

Flexibility Experienced High Quality Bioinformatics
The flexibility to prepare libraries and analyze data according to your needs. Extensive experience in dealing with numerical samples and data analysis. Generating high quality data with a guaranteed Q30≥ 80%. Employing Industry standard software and in-house bioinformatics pipelines.

Project Workflow

Sample Preparation

1. Sample Preparation

RNA purification; quality assessment and quantification

Library Preparation

2. Library Preparation

Ribosomal RNA Removal
250~300 bp Insert cDNA Library

Next-generation Sequencing

3. Sequencing

Illumina Novaseq, PE 150
≥ 40 million read pair per sample

Advanced Data Analysis

4. Data Analysis

Visualize and preprocess results, and perform custom bioinformatics analysis.

circRNA Seq

Bioinformatics Analysis Pipeline

In-depth data analysis:

  • Mapping to genome
  • Identify back-splicing junction (BSJ) reads
  • circRNA identification and profiling
  • Quantification and differential expression of circRNAs
  • Interaction with miRNAs and functional analysis
  • Target gene prediction

Sample Requirements

RNA sample (quantity ≥ 5 μg, concentration ≥ 300 ng/μL)

RIN ≥ 7.0, with smooth baseline; OD260/280: 1.8-2.2; OD260/230: ≥ 1.8.

Sample storage: RNA can be dissolved in ethanol or RNA-free ultra-pure water and stored at -80°C. RNA should avoid repeated freezing and thawing.

Shipping Method: When shipping RNA samples, the RNA sample is stored in a 1.5 mL Eppendorf tube, sealed with sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: raw data as BAM files, coverage summary, QC report, custom bioinformatics analyses.

References:

  1. Zhang J, Chen S, Yang J, et al. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nature communications, 2020, 11(1): 1-14.
  2. Xiong D, Feng Z, Lai Z, et al. High throughput circRNA sequencing analysis reveals novel insights into the mechanism of nitidine chloride against hepatocellular carcinoma. Cell death & disease, 2019, 10(9): 1-16.
  3. Liu Z, Ran Y, Tao C, et al. Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex. Genome biology, 2019, 20(1): 1-16.
* For Research Use Only. Not for use in diagnostic procedures.


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