The effect of lncRNA PART1 knockdown on gene expression in HCC1806 and HCC1395 cells

PART1 was knocked down down using GapmeRs specific to PART1. The breast cancer cells used in this study were confirmed to have PART1 expression by qPCR and knockdown of PART was confirmed by qPCR. To assess the transcriptome post PART1 knockdown, microarray analyses were completed on HCC1806 and HCC1395 cells treated with either control GapmeR, GapmeR#1 or GapmeR #2 for 48 hours and then collected in TRIzol reagent before RNA purification, and RNA purification was performed. Samples (in triplicate; n=3) were sent to the Microarray Facility, The Centre for Applied Genomics (TCAG), The Hospital for Sick Children (Toronto, Canada) where the processed for reverse transcribed into cDNA and hybridization ed to an Affymetrix Human Gene 2.0 ST microarray platform, and gene expression differences quantified. Data was collected in raw CEL format and processed through the Transcriptome Analysis Console (Affymetrix) to reveal differential gene expression.