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Formalin-Fixed, Paraffin-Embedded (FFPE) material is very heterogeneous and highly variable in terms of quality, degree of cross-linking, and accessibility of the mRNA. Therefore, processing degraded or FFPE RNA with QuantSeq-Pool may lead to uneven read distribution between samples in sequencing experiments. For best practice, the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (Cat. No. 015, 113 – 115, 129 - 131) is recommended for processing FFPE samples as it allows quality control and quantification of individual libraries. This offers the possibility to re-adjust individual samples for equimolar lane pooling and balanced read distribution during sequencing.