GSM7784675: 55_Residual_Disease; Homo sapiens; RNA-Seq
Total RNA was isolated from 295 formalin-fixed paraffin-embedded (FFPE) tissue specimens; each sample consisted of seven 4µm sections scraped from individual slides. Paraffin wax was removed with two rounds of xylene extraction. Samples were incubated in lysis buffer containing proteinase-K, and RNA was purified using miRNeasy FFPE (QIAGEN) kits following the manufacturer's recommended procedure. RNA purity and concentration were measured by UV absorbance. RNA integrity (fragment size) was assessed using a 2100 Bioanalyzer (Agilent Technologies) and RNA 6000 Nano and 6000 Pico kits. DV200 values (% fragments > 200 bases) were calculated using the 2100 Bioanalyzer Expert Software (Agilent Technologies). DV200 values ranged from 7 to 66% with 221 samples having a value ≥ 30%. Libraries were prepared using the Illumina RNA with Enrichment, Tagmentation protocol (Illumina) with the Illumina Exome Panel - Enrichment Oligos (Illumina). Libraries were profiled on a Bioanalyzer (Agilent) and quantified with an NGS Quantification Kit (Roche/Kapa Biosystems) using a StepOnePlus Real Time PCR Workstation (Thermo/ABI).