Transcriptomics
of FFPE
and other
low-quality
samples

Typically, RNA isolated from formalin-fixed, paraffin-embedded (FFPE) tissue is partially degraded and has a low overall quality.

We use the Lexogen QuantSeq 3′ mRNA-Seq Library Prep on FFPE samples. This is a cheap and ideal approach for genome wide analysis of gene expression studies, starting from total RNA as input material. The required input amount of total RNA is as low as 100pg. A high throughput version of the kit, with Illumina compatible dual indexing allows up to 9216 samples to be multiplexed in one lane.

Alternatively, we can use the Truseq Exome RNA kit for low quality samples. The kit provides a low-cost solution for analyzing (human) RNA. Starting from as little as 10 ng total RNA from intact samples or 20 ng total RNA from degraded samples, it is possible to achieve accurate, sensitive RNA-Seq results. Combining proven RNA library prep chemistry with efficient sequence-specific capture, the Truseq Exome RNA kit generates RNA-Seq libraries from degraded samples that focus on the RNA coding regions.