Can you do RNA Seq on FFPE?

In examining a large cohort of FFPE patient samples for RNA sequencing we found that 86% of extracted RNA was successfully prepared for library prep and 94% of those samples had a sufficient amount of non-ribosomal RNA, resulting in an overall RNA sequencing success rate of 81%.

What is an FFPE sample?

FFPE is a form of preservation and preparation for biopsy specimens that aids in examination, experimental research, and diagnostic/drug development. A tissue sample is first preserved by fixing it in formaldehyde, also known as formalin, to preserve the proteins and vital structures within the tissue.

What is the purpose of Transcriptomics?

The key aims of transcriptomics are: to catalogue all species of transcript, including mRNAs, non-coding RNAs and small RNAs; to determine the transcriptional structure of genes, in terms of their start sites, 5′ and 3′ ends, splicing patterns and other post-transcriptional modifications; and to quantify the changing …

What is in situ Transcriptomics?

In situ transcriptomics methods utilize the binding of fluorescent probes to specific RNA target molecules with high complementarity within cultured cells and tissue sections.

What is whole transcriptome sequencing?

Whole transcriptome sequencing comprises the measurement of the complete complement of transcripts in a sample, at a given time.

What is FFPE stand for?

Formalin-Fixed Paraffin-Embedded
FFPE stands for “Formalin-Fixed Paraffin-Embedded” and describes the two key features of this method of tissue preservation.

What is RNA transcriptomics?

Transcriptomics is the analysis of the RNA transcripts produced by the genotype at a given time that provides a link between the genome, the proteome, and the cellular phenotype. It is a global approach, which together with genomics, proteomics, and metabolomics has evolved in recent years.

What is RNA transcriptome?

A transcriptome is the full range of messenger RNA, or mRNA, molecules expressed by an organism. The term “transcriptome” can also be used to describe the array of mRNA transcripts produced in a particular cell or tissue type.

What is in situ sequencing?

In situ sequencing (ISS) is a new method by which mRNA is sequenced directly in a section of fixed tissue or cell sample. The key to ISS’s power is the linkage between sequencing information and its location—in some cases, subcellular location.

What is RNAScope?

RNAScope is a commercially available RNA in situ hybridization (ISH) that allows visualization of single RNA molecules in individual cells in a variety of sample types including formalin fixed paraffin-embedded tissue (25).