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.