Human transcriptome microarray

The goal of this study was to identify lncRNAs upregulated in LUAD that contributed to the metastasis of LUAD and positively related to poor prognosis. Total RNA was extracted from three LUAD tissue samples and three matched normal adjacent lung tissues using the RNeasy mini kit (Qiagen, Valencia, CA, USA) and quantified using Nanodrop ND-100 Spectrophotometer (Thermo Fisher Scientific, USA). RNA samples were then subjected to RNA amplification using the Sensation Plus FFPE Amplification and WT Labeling Kit (Affymetrix Inc., Santa Clara, CA, USA), as previously reported [37, 38]. The biotin double-stranded cDNA products were hybridized to Affymetrix HTA 2.0 arrays using an Affymetrix hybridization kit. Hybridized HTA 2.0 arrays were scanned with an Affymetrix GeneChip^® 3000 fluorescent scanner. Image generation and feature extraction was performed using Affymetrix GeneChip Command Console Software. The raw data (.*CEL) were analyzed using the Transcriptome Analysis Console (TAC) 4.0 software, which allows for the identification of differentially expressed genes (DEG) and exons and the visualization of alternative splicing events for determining possible transcript isoforms that may exist in samples.

To explore CAR10 expression in other databases, we downloaded Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) datasets {"type":"entrez-geo","attrs":{"text":"GSE19188","term_id":"19188"}}GSE19188 (including 45 LUAD tissue samples and 65 normal lung tissue samples) and {"type":"entrez-geo","attrs":{"text":"GSE30219","term_id":"30219"}}GSE30219 (including 85 LUAD tissue samples and 14 normal lung tissue samples). These two microarray (based on Affymetrix U133 Plus 2.0) gene expression included 3053 lncRNAs [39], we reanalyzed the expression of CAR10 between LUAD tissue samples and normal lung tissue samples. The Kaplan–Meier survival analysis of CAR10 in LUAD tissue samples was executed in GEO datasets {"type":"entrez-geo","attrs":{"text":"GSE19188","term_id":"19188"}}GSE19188 and {"type":"entrez-geo","attrs":{"text":"GSE30219","term_id":"30219"}}GSE30219.