Open Access Methodology

The chemiluminescence based Ziplex® automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip® expression profiles

Michael CJ Quinn1, Daniel J Wilson2, Fiona Young2, Adam A Dempsey2, Suzanna L Arcand3, Ashley H Birch1, Paulina M Wojnarowicz1, Diane Provencher456, Anne-Marie Mes-Masson46, David Englert2 and Patricia N Tonin137*

Author Affiliations

1 Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada

2 Xceed Molecular, Toronto, M9W 1B3, Canada

3 The Research Institute of the McGill University Health Centre, Montréal, H3G 1A4, Canada

4 Centre de Recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montréal, H2L 4M1, Canada

5 Département de Médicine, Université de Montréal, Montréal, H3C 3J7, Canada

6 Département de Obstétrique et Gynecologie, Division of Gynecologic Oncology, Université de Montréal, Montreal, Canada

7 Department of Medicine, McGill University, Montreal, H3G 1A4, Canada

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Journal of Translational Medicine 2009, 7:55  doi:10.1186/1479-5876-7-55

Published: 6 July 2009

Additional files

Additional file 1:

Sample description. RNA samples used in the expression analyses.

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Additional file 2:

Genes for normalization. Differential expression between NOSE and TOV in the raw data (log2 ratios, and T-test).

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Additional file 3:

Correlations between different probe designs for the same target gene. Three different probes were designed and tested for each of the target genes, except for one of the genes (APOE) for which there were two designs. Each row of plots contains correlations between probes for a given gene. The accession numbers and gene symbols are indicated on the plots. Plots with linear scales are shown on the left, and plots with log10scales are shown on the right. The probes are identified in the axis labels with an Xceed part number and the gene symbol. The distance of each probe from the 3' end of the sequence corresponding to the accession number is shown after the colon in the axis labels. The colors used to plot the data for each sample are: NOSE samples – blue, TOV samples – red, cell line samples – green. Low intensity probes are plotted with open symbols.

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Additional file 4:

Signal intensities and 3'/5' ratios for all ten 5' control probes on duplicate chips. 3', 5' signial intensities and 3'/5' ratios for each sample, for the genes RPL4, POL2RA, ACTB, GAPD and ACADVL2.

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Additional file 5:

RNA quality control. Correlation between the geometric mean of seven 3'/5' control probe ratios and RIN number or 28 S/18 S ratios. Samples MG0001 (TOV-21G) and MG0026 (NOSE-1181) are not included.

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Additional file 6:

Correlations between Affymetrix U133A and Xceed Ziplex data. Correlation graphs plotted for all 93 study genes, organized alphabetically. TOV samples are shaded red, NOSE blue and cell lines are indicated in green.

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Additional file 7:

Correlation analysis of Ziplex versus Affymetrix gene expression data. Correlation analysis for all genes including p-value and R-squared.

Format: XLS Size: 41KB Download file

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