FFPE RNA-Seq

Leveraging our technology for low-quality RNA samples, CD Genomics provides RNA sequencing services for Formalin-Fixed Paraffin-Embedded (FFPE) tissues to help you discover critical information in preserved samples. Utilizing an optimized high-throughput sequencing process, our FFPE RNA-Seq service enables gene expression studies on small sample amounts and reliable detection of low-expressed genes with accuracy and integrity of transcriptome data, which can be applied in biomarker discovery, disease diagnostic research, precision therapy development, and more.

Overview

Transcriptome sequencing is increasingly applied in pre-clinical and clinical research to provide important information on gene expression regulation and mechanism, as well as allele-specific expression profiling, fusion detection, mutation detection, and therapy selection. A variety of technologies have been developed for the detection of clinical or preclinical samples, such as blood transcriptome sequencing, biofluid RNA sequencing, and other RNA sequencing methods for fresh frozen tissues. The FFPE process is currently the standardized method for long-term preservation of samples, and is commonly used to preserve a large resource of clinically diseased and normal tissue samples. However, FFPE samples are often precious and have a long shelf life, suffering from low RNA volume and high degradation, which make it difficult to use standard RNA sequencing techniques. CD Genomics has established a next generation sequencing based solution dedicated to low-quality RNA samples and small sample amounts, including FFPE tissue RNA-seq services, by optimized experimental manipulation methods and bioinformatic analysis techniques. Our services can focus on both coding RNA regions (mRNA) and total RNA, and can meet the needs of a diverse range of medical research biological samples.

Features

Accurate & Effective High Sensitivity Bioinformatics Analysis One-Stop Solution
This method is ideal for RNA-Seq with FFPE or degraded samples. Efficient rRNA removal for accurate and sensitive transcript detection. Our integrated bioinformatics pipeline can be tailored to suit your project, data visualization. One-stop solution from sample QC, library construction, to sequencing and data analysis.

Project Workflow

Sample Preparation

1. Sample Preparation

Quality assessment and quantification

Library Preparation

2. Library Preparation

cDNA stranded library preparation; library QC.

Sequencing

3. Sequencing

llumina NovaSeq 6000; PE 50/75/100/150; 40 Million Reads.

Data Analysis

4. Data Analysis & Delivery

Visualize and preprocess results, and custom bioinformatics analysis.

Bioinformatics Analysis Pipeline

De novo Transcriptome Sequencing

In-depth data analysis:

  • Biostatistical analysis –transcript copy number comparisons, expression analysis, length distribution, multi-parameter data analysis, etc.
  • GO and KEGG enrichment analysis
  • Functional Annotation
  • Detect novel and rare transcripts
  • Splicing analysis
  • SNP/InDel analysis
  • Fusion analysis

Sample Requirements

FFPE Sample (≥ 10, ≥ 25 mm2, recommended cryopreservation)

RNA sample (≥ 200 ng, 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 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 a 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 report.

References:

  1. Newton Y, Sedgewick AJ, Cisneros L, et al. Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples. Scientific reports, 2020, 10(1): 1-11.
  2. Pennock ND, Jindal S, Horton W, et al. RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery. BMC medical genomics, 2019, 12(1): 1-18.
* For Research Use Only. Not for use in diagnostic procedures.


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