GSM5502700: GCB_4; Homo sapiens; RNA-Seq
Total DNA/RNA was harvested from three or four 10 μm thickness scrolls from FFPE blocks kept in our biobank. We used AllPrep® DNA/RNA FFPE kit (Qiagen). To determine COO of DLBCL samples we applied a digital analyzer in NanoString platform (NanoString Technologies, WA). After processing on the nCounterTM Prep Station and acquiring the gene expression data on the nCounterTM Digital Analyzer at the “high resolution” setting, raw data files were analyzed using the RUO version of the NanoString Lymphoma Subtyping Test (LST) algorithm. The Ribo-Zero RNA removal kit for Human (Illumina Inc.) was used to deplete rRNA. We prepared cDNA libraries after rRNA were depleted from samples. We used the TruSeq Stranded mRNA Library Prep (Illumina Inc.) together with the Superscript III Reverse Transcriptase (Thermo Fisher Scientific). samples indexed with compatible indices were run together on a NextSeq 500 instrument (Illumina inc.) with a 2x150 bp paired-end protocol RNA libraries were prepared for sequencing using standard Illumina protocols