HOTAIRM1 knockdown microarray

To investigate the target genes of HOTAIRM1 in glioma cells, we conducted a lncRNA + mRNA expression microarray analysis to identify novel HOTAIRM1 regulating genes. Three glioma cell lines U87MG, T98G and A172 stably knockdown HOTAIRM1 were used as the experiments models. We conservatively established a minimum of 2-fold difference between shHOTAIRM1 (knockdown HOTAIRM1) and shNT (control group), and identified 10 up-regulated and 22 down-regulated genes that met the threshold in all cell lines. Total RNAs from ～106 shNT-U87MG, shHOTAIRM1-U87MG, shNT-T98G, shHOTAIRM1-T98G, shNT-A172 and shHOTAIRM1-A172 cells were extracted using TRIzol reagent (Invitrogen, USA). The RNA integrity was measured at an Agilent Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA). The qualified total RNA was further purified by using a NucleoSpin RNA clean-up kit (740.948.250, Macherey-Nagel). cRNA was synthesized and then cDNA was reverse transcribed and purified with Nucleospin Extract Ⅱ (740.609.250, Macherey-Nagel). The labelled cDNA was used for hybridization on the Genechip Agilent Human lncRNA 4 × 180 K array (Agilent Technologies). The slides were scanned in an Agilent Microarray Scanner (Agilent Technologies) under the default settings in CapitalBio Corporation. Quantile algorithm (Gene Spring Software 11.0, Agilent Technologies) was used for the raw data normalization.