Human lncrna mrna expression microarray version 3

The ArrayStar Human LncRNA/mRNA Expression Microarray Version 3.0 (Array-Star, Inc., Rockville, MD, USA) was used, which includes w30 586 lncRNA probes and 26 109 mRNA transcripts and was constructed from six publicly available transcriptome databases and selected lncRNA publications (Arraystar Human LncRNA Array V3.0, available at www.arraystar.com/ microarray/service_main.asp?id=198, accessed 12/7/2014). In the microarray profiling, the RNA labelling, microarray hybridisation, slide washing and scanning were performed based on the standard protocols of ArrayStar. Acquired array images were analysed using the Agilent Feature Extraction Software (version 11.0.1.1). Quantile normalisation and subsequent data processing were performed using the GeneSpring GX Version 12.0 Software (Agilent Technologies). After quantile normalisation of the raw data, lncRNAs/mRNAs present in at least 15 out of 21 samples were chosen for further data analyses. A selection criterion of statistical significance calculated as a corrected P value of !0.05 using the Benjamini Hochberg false discovery rate method along with a minimum fold change cut-off of 2.0 (up-or downregulated) was applied to identify differentially expressed lncRNAs/mRNAs.