RNA Sequencing

FFPE RNA Sequencing

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FFPE RNA Sequencing Services

Profiling of Archival Tissue Samples

FFPE RNA-seq is a powerful tool for gene expression profiling of archival tissue samples. The FFPE RNA sequencing services can be used for bulk, single cell, and spatial profiling. At SeqMatic, FFPE RNA-seq is used in studies related to the progression of disease and to identify potential biomarkers for diagnosis and treatment.

Service Features

Research Approach –

FFPE can be used for bulk total RNA, single cell RNA, and VISIUM spatial RNA profiling.

Stringent Quality Controls –

SeqMatic qualifies RNA with a TapeStation Electropherogram for each total RNA sample submitted. A TapeStation analysis includes a RNA Integrity Number (RIN) and DV200 for each sample, which establishes relative length as a measure of RNA quality. Results are shared for review and approval prior to proceeding to library preparation.

High-Quality design considerations for read depth –

SeqMatic has recommendations for different research approaches:

For FFPE Bulk Total RNA-seq we recommend 50 to 60M reads per sample.
For 10x Genomics Flex FFPE we recommend 10K reads per cell (per 10x Genomics protocol)
For 10x Genomics Visium spatial transcriptomics we recommend 25K read pairs per spot covered

Higher and lower read depths are available depending on project needs

Preliminary Sequencing –

After library preparation, libraries are pooled in equal volumes and the final pool is quantified by Agilent TapeStation and checked via preliminary sequencing (MiSeq). Libraries are then normalized and re-pooled based on the read number from the preliminary sequencing dataset.

Histopathology –

Full service histopathology laboratory available.

World-class validation standard & practices –

SeqMatic is equipped to ensure accurate, repeatable and reproducible results. SeqMatic’s quality program has been audited and approved as part of becoming a Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP) certified sequencing facility. Our CLIA quality program requires the use of well-defined protocols to maintain the consistency and reproducibility of our NGS workflows. Thus, the samples will be processed in a CLIA environment.

Custom assay services –

Our highly personalized sequencing services can be adapted to almost any (high and/or low throughput) sequencing workflow required by our customers so that we optimize the quality and quantity of data output.

FFPE RNA Sequencing – Service Highlights