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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 LUTHOR HD Pool may lead to uneven read distribution between samples in sequencing experiments.
For best practice, the QuantSeq FFPE FWD 3' mRNA-Seq Library Prep Kit for Illumina (Cat. No. 222 - 223) is recommended for processing FFPE samples, as it allows quality control and quantification of individual libraries.