Computational protocol: Solanum Incanum Extract Downregulates Aldehyde Dehydrogenase 1-Mediated Stemness and Inhibits Tumor Formation in Ovarian Cancer Cells

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Protocol publication

[…] Total RNA was isolated using the RNeasy Micro Kit (Qiagen; Valencia, CA, USA), quantified, and checked for quality with a Bioanalyzer 2100 system (Agilent; Palo Alto, CA, USA). Labeled probes for Affymetrix DNA microarray analysis were prepared according to the manufacturer's instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix U133A GeneChip arrays (22,283 probe sets, Santa Clara, CA, USA) at 45ºC for 16 h, and then washed and stained using GeneChip Fluidics. The arrays were scanned to a target intensity of 500 by a GeneArray Scanner, and patterns of hybridization were detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes. Image acquisition and probe quantification was performed using Affymetrix GeneChip Operating Software. Microarray quality control was performed using R package affyQCReport software . The gcrma function in the R package affy was applied to normalize the CEL files using the RMA method . Data are MIAME compliant and have been deposited in the Gene Expression Omnibus. […]

Pipeline specifications

Software tools affyQCReport, affy
Databases GEO
Application Gene expression microarray analysis
Organisms Homo sapiens, Mus musculus
Diseases Neoplasms, Ovarian Neoplasms, Keratosis, Actinic
Chemicals Acetaldehyde, Cisplatin, Paclitaxel