Human lncrna expression microarray

The total RNA was purified using an RNeasy Mini kit (Qiagen GmbH, Hilden, Germany) and labeled with a Quick Amp Labeling kit (Agilent Technologies, Inc., Santa Clara, CA, USA). Labeled RNA was purified again using the RNeasy Mini kit. The RNA was subsequently hybridized onto an Arraystar Human lncRNA Expression Microarray (version 4.0; Arraystar, Inc., Rockville, MA, USA), which was designed for 30,586 lncRNAs and 26,109 coding genes based on the RefSeq (https://ncbi.nlm.nih.gov/refseq/), UCSC Known Genes and Gencode (https://genome.ucsc.edu/) and Ensembl databases (http://ensemblgenomes.org/). Agilent Feature Extraction software (version 11.0.1.1; Agilent Technologies, Santa Clara, CA, US) was used to analyze the acquired array images. The microarray data were deposited in the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession no. GSE124352. Differentially expressed lncRNAs and mRNAs were identified to be statistically significant (fold change >2.0 or <-2.0; P<0.05) using a paired t-test. The microarray was performed by Kangchen BioTech Co., Ltd. (Shanghai, China). Subgroup analysis was conducted to classify the differentially expressed lncRNAs according to their expression levels.

The microarray contained 8,277 lncRNA probes, which were designed by Arraystar Human LncRNA Expression Microarray (version 4.0; Arraystar, Inc., Rockville, MA, USA), based on the RefSeq (http://www.ncbi.nlm.nih.gov/refseq/), UCSC Known genes (http://genome.ucsc.edu/), and Ensembl (http://ensemblgenomes.org/)databases and associated literature (19 (link),20 (link)); 32,207 protein-coding transcripts were used for microarray assays in three PCa tissue samples and their matched non-tumor samples. Differentially expressed lncRNAs and mRNAs, found to be statistically significant [P<0.05; fold-change (FC)>2] between the two groups were identified by comparing the normalized expression levels in the tumor and non-tumor samples using a paired t-test. Hierarchical clustering was then performed to analyze the differential lncRNA and mRNA expression patterns.