Cell-Free RNA-Seq (cfRNA-seq)

CD Genomics provides a battery of biofluid profiling services utilizing next-generation sequencing technology. Our services can complement mainstream sequencing methods to investigate the levels of RNA molecules in biofluid samples, explore poorly characterized, rare transcripts and mutations. Cell-free RNA sequencing (RNA-seq) is a tool that extracts, processes, and analyzes cell-free RNA. We have developed a complete, automated workflow for performing cell-free RNA-seq. Our services are fully customizable to your research needs.

Overview

Cell-free RNA (cfRNA) naturally occurs in cell free fluids and sheds from tumor cells. CfRNA in plasma usually consists of degradative small RNA with size smaller than 200 nt, and plays an important role in cell communications. Its biogenesis and distribution are correlated with physical and pathological situations. Therefore, cfRNA has been considered as useful biomarkers for disorder diagnosis and prognosis and potential targets for disease interventions. Circulating tumor cells (CTCs) and plasma cfRNA can serve as biomarkers for prognosis and treatment response in cancer. While sometimes CTCs are undetectable, the measurement and analysis of cfRNA provide a feasible tool for the screening or diagnosis of diseases and the monitoring of therapy. Cell-free RNA-seq is a powerful approach that extracts cfRNAs from human blood plasma or serum and constructs high quality, stranded libraries for next-generation sequencing (NGS). CD Genomics offers automated and optimized end-to-end solutions with minimized errors, reduced hand-on time, and increased throughput and reproducibility. Our services are flexible and tailored to your research needs.

Project Workflow

Bioinformatics Analysis Pipeline

In-depth data analysis:

• Biostatistical analysis –transcript copy number comparisons, expression analysis, length distribution, multi-parameter data analysis, etc.
• Identification of differentially expressed transcripts
• RNA structure analysis
• Target gene prediction and functional analysis
• GO and KEGG enrichment analysis
• Detect novel and rare transcripts and mutations
• Novel transcript prediction

Sample Requirements

RNA sample extracted from plasm or other biofluids (concentration ≥ 50 ng/uL, quantity ≥ 1 ug)

1.8 ≤ OD260/280 ≤ 2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0.

Please make sure that the RNA is not significantly degraded.

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: FastQ, BAM, coverage summary, QC report, custom bioinformatics analysis.

Reference:

1. Yang X, Wang T, Zhu S, et al. PALM-Seq: simultaneous sequencing of cell-free long RNA and small RNA. bioRxiv, 2019: 686055.