Expression data from glioma stem cells (GSC), comparing the WT cells to those after ALDH1A3-KO

Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs potentially regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). ALDH1A3 is the dominant isomer of the ALDH gene family in Mesenchymal subtype of GSC cells and is highly upregulated compared to other subtype of GSCs. ALDH1A3 is an important enzyme in the synthesis of Retinoic Acid, which regulates various downstream pathways and the transcription of numerous genes. Microarray analysis of the GSCs before or after depletion of ALDH1A3 provides important information to determine the genes regulated by ALDH1A3 in the mesenchymal subtype of GSCs. We used microarrays to analyze the transcriptome change after the depletion of ALDH1A3 in GSC-326 cells that express very high levels of ALDH1A3. We depleted ALDH1A3 in GSC-326 cells using the CRISPR/Cas9 technique with 3 diffirent gRNAs targeting different regions of the ALDH1A3 gene. Six ALDH1A3-KO single clones generated from 3 diffirent gRNAs have validated the loss of ALDH1A3 protein expression. Total RNA was extracted from the six ALDH1A3-KO single clone cells and three ALDH1A3 wlid type control cells. The RNAs were then processed using the kits for the Affymetrix GeneAtlas system and labeled cRNAs were hybridized to Affymetrix Human Genome U219 Array Strip to profile the transcriptome change after the loss of ALDH1A3.