Samples were lysed (RNeasy Lysis Buffer, Qiagen, Hilden, Germany) and homogenised (TissueLyser II, Qiagen, Hilden, Germany) prior to RNA extraction.
Growth protocol
Endobronchial biopsy samples were placed in RNA-later (Qiagen, Hilden, Germany) for storage at -20 °C prior to RNA extraction.
Extracted molecule
total RNA
Extraction protocol
RNA extraction was perfomed using (RNeasy Mini Kit and RNAse-free DNAse, Qiagen, Hilden, Germany). RNA was quantified (Quant-iT RiboGreen RNA Quantitation Assay Kit, Life Technologies Corporation, USA)
Label
biotin
Label protocol
biotin
Hybridization protocol
750 ng of cRNA was hybridized to Illumina’s HT-12 V4 Beadchips
Scan protocol
BeadChips were scanned using the Illumina Bead Station and data was captured using BeadScan 3.5.11 (Illumina, San Diego, USA).
Description
200598770012_L
Data processing
Array raw data were processed using GenomeStudio software, Illumina and analysed using R Bioconductor lumi and limma packages. Sample and gene profiling results were included in the analysis if the sample was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and data passed quality control criteria in R during analysis. Data was log2‐transformed and quantile‐normalised.
