Journal: The Journal of Biological Chemistry

Article Title: O -Linked β- N -Acetylglucosaminylation ( O -GlcNAcylation) in Primary and Metastatic Colorectal Cancer Clones and Effect of N -Acetyl-β- d -glucosaminidase Silencing on Cell Phenotype and Transcriptome *

doi: 10.1074/jbc.M112.345546

Figure Lengend Snippet: Summary of IPA performed for cDNA microarray analysis of the siOGA-SW620 and pS-SW620 clones

Article Snippet: Microarray CEL files were read into Partek and preprocessed by Robust Multiarray Averaging ( 23 ) using default parameters, followed by quantile normalization and probe summarization using median polish.

Techniques: Microarray, Clone Assay

Journal: The Journal of Biological Chemistry

Article Title: O -Linked β- N -Acetylglucosaminylation ( O -GlcNAcylation) in Primary and Metastatic Colorectal Cancer Clones and Effect of N -Acetyl-β- d -glucosaminidase Silencing on Cell Phenotype and Transcriptome *

doi: 10.1074/jbc.M112.345546

Figure Lengend Snippet: OGA silencing affects the transcriptome of SW620 metastatic CRC clone. Control pS-SW620 cells and OGA-silenced SW620 cells were subjected to cDNA microarray analysis. Gene Ontology-based over-representation for the microarray dataset was performed with the IPA software. Over-represented genes were categorized according to their functions (A), and canonical pathways were annotated using the KEGG database (B).

Article Snippet: Microarray CEL files were read into Partek and preprocessed by Robust Multiarray Averaging ( 23 ) using default parameters, followed by quantile normalization and probe summarization using median polish.

Techniques: Control, Microarray, Software

Journal: The Journal of Biological Chemistry

Article Title: O -Linked β- N -Acetylglucosaminylation ( O -GlcNAcylation) in Primary and Metastatic Colorectal Cancer Clones and Effect of N -Acetyl-β- d -glucosaminidase Silencing on Cell Phenotype and Transcriptome *

doi: 10.1074/jbc.M112.345546

Figure Lengend Snippet: Experimental validation of microarray data for four selected proteins. Total proteins were extracted from pS-SW620 and siOGA-SW620 cells and analyzed for the levels of four proteins that showed altered regulation by cDNA microarray assay. A, left panel, representative Western blots using anti-E-cadherin, β-catenin, caveolin-1, IκB-β, and actin antibodies. Right panel, quantitative analysis of the protein levels in the two cell lines. B, total proteins were extracted from SW620 cells (control) and from SW620 cells treated with 25 μm TMG for 24 h (TMG) and analyzed for the level of the above-mentioned proteins. Left panel, representative Western blots. Right panel, quantitative analysis of the relative protein levels in the two samples. All quantitative results (A.U., arbitrary units) are expressed as the mean ± S.E. of at least three repeats. Asterisks indicate significant difference between clones (p ≤ 0.05).

Article Snippet: Microarray CEL files were read into Partek and preprocessed by Robust Multiarray Averaging ( 23 ) using default parameters, followed by quantile normalization and probe summarization using median polish.

Techniques: Biomarker Discovery, Microarray, Western Blot, Control, Clone Assay