Total RNA was extracted from 2mm punch biopsies of FFPE tissue using the RNeasy FFPE kit (Qiagen, Doncaster, VIC, Australia).
Label
Biotin
Label protocol
standard affymetrix protocol
Hybridization protocol
100ng total RNA of all FFPE samples was amplified (Ovation FFPE WTA kit) and biotinylated (Encore Biotin module) according to the manufacturers’ instructions (Nugen, San Carlos, California, United States). The samples were hybridised to HuGene 2.0 arrays (Affymetrix, Santa Clara, California, United States) and 17 hours later washed and stained.
Scan protocol
The Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).
Description
Gene expression data from TNBC patients grade 3
Data processing
The HumanGene 2.0 arrays (Affymetrix) contain probe features representing 11,000 lncRNAs, 24,000 genes, and 30,000 coding transcripts. The data was imported to Genomic Suite 6.6 (Partek) and a robust multi-array analysis (RMA) was performed, which included log2 transformation, background correction, quantile normalisation and summarisation of the probe features resulting in a set of expression signal intensities.
