title: GSM4878462: SMARCA4 mutated ATRT Case 12 [SMARCA4f]; Homo sapiens; RNA-Seq
library_construction_protocol: For RNA isolation from FFPE tissue, 10 x 10 µm sections were cut and RNA isolated using the Maxwell® RSC RNA FFPE Kit (Promega). The RNA integrity was analyzed with the RNA 6000 Nano Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). From total RNA, the ribosomal RNA was depleted with the help of the RiboCop rRNA Depletion Kit (Lexogen). The RNA sequencing library was generated using the CORALL Total RNA-Seq Library Prep Kit (Lexogen). Concentrations of all samples were measured with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and fragment lengths distribution of the final libraries was analyzed with the DNA High Sensitivity Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples were normalized to 2 nM and pooled at equimolar concentrations. The library pool was sequenced on the NextSeq500 (Illumina) with 1 x 75 bp, with 24.5 to 35.1 million reads per sample.