GSM6210088: LMU_Pat_64; Homo sapiens; RNA-Seq
After histopathological review, simultaneous DNA and total RNA extraction of serial formalin-fixed and paraffin-embedded tissue sections was performed using the AllPrep DNA/RNA FFPE Kit RNA isolation (Qiagen, Hilden, Germany). Isolated RNA was quantified using a Qubit Fluorometer and RNA integrity was assessed determining DV200 values (percentage of fragments >200 nucleotides) using the 2100 Bioanalyzer followed by categorization into low, medium, and good quality samples. For whole RNA sequencing, sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., USA). Input quantity and initial RNA fragmentation time was adjusted to the respective RNA quality. After library preparation, library quality and quantity were evaluated using the Quanti-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, MA, USA) and the Bioanalyzer High Sensitivity DNA Analysis Kits (Agilent Technologies).