FFPE RNA Sequencing
Get trustworthy RNA-Seq data from your FFPE samples, even degraded ones
Find the ideal service for your application:
FFPE RNA Sequencing
Formalin-fixed paraffin-embedded (FFPE) tissue samples are a precious source of molecular information, heavily utilized in fields such as cancer research, oncology, immunology, hematology etc. Next-generation sequencing of FFPE samples provides transcriptional profiles of healthy vs. diseased tissue, giving insights into disease development, progression, and treatment efficacy.
RNA-Seq from FFPE samples can be notoriously challenging due to chemical modifications of RNA, cross-links with other molecules, degradation of RNA, gDNA contamination, and the limited accessibility of RNA.
Lexogen’s FFPE RNA Sequencing service provides excellent, cost-efficient transcriptome profiling from FFPE samples or any other degraded, low-quality, and low input RNA samples. Our success in processing these complex samples comes from years of hands-on experience and well-established and optimized workflows.
Our end-to-end service includes everything from RNA extraction from FFPE curls to library preparation (for gene expression profiling or whole transcriptome sequencing), ending with tailor-made data analysis.
Benefits
- Years of hands-on experience with low-quality FFPE RNA
- Compatible with low input FFPE material
- Well-established workflows for FFPE RNA-Seq
- Ideal for large scale high-throughput screening projects
Applications
- Cost-efficient FFPE gene expression profiling
- Whole Transcriptome Sequencing of FFPE samples, e.g., for detection of fusion genes, isoforms, SNPs etc.
- Analysis of non-coding transcripts, including lncRNA, snRNA, snoRNA, circRNA, etc.
- High-throughput FFPE gene expression sequencing
- Targeted FFPE RNA sequencing
- Drug discovery & development studies, e.g., target validation, biomarker identification
Deliverables
- Demultiplexed files (FASTQ)
- Trimmed files (FASTQ)
- Aligned files (BAM)
- Rseqc (.txt)
- Gene counts and counting summary (.tsv)
- Differential expression and DE summary (.tsv)
- Multiqc reports – raw, trimmed, alignment, rseqc (.html)
- PCA plot
- Deliverables summarized in a PDF report
Working with us
Consultations
- Together we will identify the best experimental design for your project.
- Shipment support (such as help with customs and export documents), or organizing the shipment under certain conditions.
Sample Extraction
- RNA extraction from FFPE curls.
- Sample QC included.
Library Preparation
- Various library preparation solutions, depending on and adapted to your specific experimental objectives.
- Library QC included.
Sequencing
- Read mode and read depth most suitable for your application.
Data Analysis and Report
- Data quality control.
- Data analysis in-house.
- Standard data analysis options, on-demand, custom-design data analyses, and custom pipeline development.
