whole human genome microarray (4 × 44 k) kit  (Agilent technologies)

Journal: PLoS ONE

Article Title: Glycogene Expression Alterations Associated with Pancreatic Cancer Epithelial-Mesenchymal Transition in Complementary Model Systems

doi: 10.1371/journal.pone.0013002

Figure Lengend Snippet: (A) RT-PCR was performed on lysates from the indicated cell lines, and intensities of the bands at the expected size for each gene were quantified. A student's t-test (results given by the p value) was performed comparing the band intensities between the mesenchymal-like cell lines (in bold) and the epithelial cell lines. In addition, a correlation was calculated (results given by the r value) between the RT-PCR results and the microarray data. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a cDNA loading control. (B) Comparison of GALNT3 protein levels by Western blot in selected pancreatic cancer cell lines. Lysates were collected from the selected cell lines, fractionated by SDS-PAGE, and probed by Western blot. Mesenchymal-like cell are labeled in bold. The highlighted bands are at the expected molecular weights of 73 kD for GALNT3 and 42 kD for actin. (C) MRC2 protein levels measured by Western blot in TGFβ treated and untreated cells. The cell lines were either exposed to 5 ng/mL TGFβ or untreated under serum starvation for 72 hours prior to cell lysis. The highlighted bands are at the expected molecular weights of ∼167 kD for MRC2 and 42 kD for actin.

Article Snippet: 96.7% of these genes are represented on the Affymetrix Human Genome U133 Plus 2.0, and 92.2% are represented on the Agilent Whole Human Genome Microarray Kit, 4×44K.

Techniques: Reverse Transcription Polymerase Chain Reaction, Microarray, Western Blot, SDS Page, Labeling, Lysis

Journal: PLoS ONE

Article Title: Glycogene Expression Alterations Associated with Pancreatic Cancer Epithelial-Mesenchymal Transition in Complementary Model Systems

doi: 10.1371/journal.pone.0013002

Figure Lengend Snippet: (A) RT-PCR was performed on lysates from the indicated cell lines, and intensities of the bands at the expected size for each gene were quantified. A student's t-test (results given by the p value) was performed comparing the band intensities between the mesenchymal-like cell lines (in bold) and the epithelial cell lines. In addition, a correlation was calculated (results given by the r value) between the RT-PCR results and the microarray data. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a cDNA loading control. (B) Comparison of GALNT3 protein levels by Western blot in selected pancreatic cancer cell lines. Lysates were collected from the selected cell lines, fractionated by SDS-PAGE, and probed by Western blot. Mesenchymal-like cell are labeled in bold. The highlighted bands are at the expected molecular weights of 73 kD for GALNT3 and 42 kD for actin. (C) MRC2 protein levels measured by Western blot in TGFβ treated and untreated cells. The cell lines were either exposed to 5 ng/mL TGFβ or untreated under serum starvation for 72 hours prior to cell lysis. The highlighted bands are at the expected molecular weights of ∼167 kD for MRC2 and 42 kD for actin.

Article Snippet: Since our glycan-related genes represented 3.0% of the total unique Agilent Whole Human Genome Microarray Kit (4×44K probes), random chance predicted a corresponding 3.0% representation of glycogenes among the list of genes that changed.

Techniques: Reverse Transcription Polymerase Chain Reaction, Microarray, Western Blot, SDS Page, Labeling, Lysis