RNA was extracted from paraffin scrolls using the RNeasy FFPE kit (Qiagen) with modification. In brief, 1 ml of xylene was first added to a 25 μm paraffin scroll, vortexed vigorously for 10 sec and centrifuged at full speed for 2 min. Supernatant was then removed and 1 ml of ethanol (100%) was added to the pellet, mixed by vortexing and centrifuged at full speed for 2 min. Supernatant was removed and the tube was incubated at room temperature from 10 min with lid opened. Subsequently, RNA was extracted using reagents provided in the RNeasy FFPE extraction kit according to the manufacturer’s instruction. Finally, purified RNA was eluted from the RNeasy MinElute spin column using 30 μl RNase-free water.
Label
biotin
Label protocol
WT-Ovation FFPE System V2 (NuGEN Inc; San Carlos, CA)
Hybridization protocol
Affymetrix protocol
Scan protocol
Affymetrix protocol
Data processing
The data were RMA normalized using Bioconductor package 'oligo' version 1.24.2.
