GSM7932833: patient 5, 100 ng input; Homo sapiens; RNA-Seq
RNA samples were extracted from formalin fixed paraffin embedded (FFPE) slides from the initial surgical resection of tumors.  Paraffin was removed from 10 unstained slides using a xylene substitute (SigmaAldrich cat# A5597), 100% ethanol, 70% ethanol, 30% ethanol and DEPC water incubation series.  Tissue was scraped from the slide into Qiagen PKD buffer (Qiagen RNeasy FFPE kit cat#73504) with Proteinase K.  This mixture was incubated at 56°C for 15min then placed on ice for 5 min.  Samples were centrifuged for 25min at max speed. The supernatant was transferred to a new tube and heated for 45min at 80°C.  RNeasy 3-4 FFPE protocol with DNAse I for Qiacube was used to extract RNA from samples. TruSeq Stranded Total RNA LP Gold (Illumina SKU: 20020598) kit, an ultra-low-input sequencing library prep, was used for creating sequencing libraries