RNA was isolated using the RNeasy® FFPE Kit (Qiagen, Hilden, Q15 Germany) according to the manufacturer’s directions. RNA concentrations and quality were measured using the Agilent 2100 BioAnalyzer (Santa Clara, CA, USA). To correct for degradation of the RNA, the percentage of fragments of 300-4000 nucleotides was used to calculate the corrected concentrations. For each sample, 300 ng of total RNA, with a maximum of 7 mL (>42.8 ng/mL), was used.
Label
n.a.
Label protocol
n.a.
Hybridization protocol
Hybridization was performed at 65°C for 17 hours using a SimpliAmp Thermal Cycler (Applied Biosystems, Foster City, CA, USA).
Scan protocol
The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).
Data processing
Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).
