title: GSM8189555: 22_1SLE-3-1C; Homo sapiens; RNA-Seq
library_construction_protocol: RNA was isolated from Formalin Fixed Paraffin Embedded (FFPE) tissue sections fixed on slides using the RNeasy DSP FFPE kit (Qiagen, Hilden, Germany). Briefly, sections 10 microns thick, were scraped from 5 slides of each sample and submerged in Deparaffinization Solution (DSP) as per protocol. During this process tissue digestion using Proteinase K was also done. DNAseI treated RNA was subsequently isolated using Qiagen's proprietary spin column method as per protocol. RNA integrity was assessed using the TapeStation RNA ScreenTape (Agilent, Santa Clara, CA) and concentration was determined used the Qubit 2.0 Fluorometer (ThermoFisher, Waltham, MA). Since FFPE RNA is expected to be highly degraded, a DV200 value, which is the percentage of RNA fragments above 200bp, was determined for each sample. Libraries for whole transcriptome RNA sequencing were prepared using the Stranded Total RNAseq with Ribo-zero Plus kit (Illumina, San Diego, CA) as per manufacturer's instructions starting with an input of 100ng of RNA and 15 cycles of final PCR amplification. Library size was assessed using the 2100 Bioanalzyer and the High-Sensitivity DNA assay (Agilent, Santa Clara, CA). Concentration was determined using the Qubit Fluorometer 2.0. Next Generation Sequencing with a paired-end 2x100bp run length was done on the NextSeq2000 platform (Illumina, San Diego, CA). A minimum of 30M reads per sample was acquired for each sample.