Computational protocol: Phenotypic Plasticity Determines Cancer Stem Cell Therapeutic Resistance in Oral Squamous Cell Carcinoma

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Protocol publication

[…] RNA was extracted using the RNeasy microkit (Qiagen) and analysed using an Illumina Human HT-12 v4 gene expression array. The results were analysed using the GenomeStudio software (Illumina), with quantile normalization and a false discovery rate filter of 5% in differential expression analysis. The top 150 differentially expressed genes from each analysis were analysed with the functional annotation clustering tool on the DAVID database (, ). Microarray data are deposited in the GEO database under the accession numbers GSE74578 and GSE74580. […]

Pipeline specifications

Software tools GenomeStudio, DAVID
Application Gene expression microarray analysis
Diseases Carcinoma, Squamous Cell, Neoplasms
Chemicals Tretinoin, Thapsigargin