Open Access Highly Accessed Research article

Evaluation of a new high-dimensional miRNA profiling platform

Julie M Cunningham1*, Ann L Oberg2, Pedro M Borralho3, Betsy T Kren4, Amy J French1, Liang Wang1, Brian M Bot2, Bruce W Morlan2, Kevin AT Silverstein5, Rod Staggs5, Yan Zeng6, Anne-Francoise Lamblin5, Christopher A Hilker1, Jian-Bing Fan7, Clifford J Steer4 and Stephen N Thibodeau1

Author Affiliations

1 Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota, USA

2 Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA

3 iMed.UL, Faculty of Pharmacy, University of Lisbon, Lisbon 1649-003, Portugal

4 Departments of Medicine and Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, Minnesota, USA

5 Biostatistics and Informatics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA

6 Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA

7 Illumina Inc. 9885 Towne Centre Drive, San Diego, California, 92121, USA

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BMC Medical Genomics 2009, 2:57  doi:10.1186/1755-8794-2-57

Published: 27 August 2009

Additional files

Additional file 1:

MVA plots: within plate cell line replicates. Pre-normalization MVA plots for within plate cell line technical replicates on all four SAMs corresponding to panel A of Figures 3 and 4. Axes are described in the manuscript.

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Additional file 2:

MVA plots: within plate patient replicates. Pre-normalization MVA plots for within plate patient technical replicates for 200 ng of extraction 1 on the first three SAMs corresponding to panel B of Figures 3 and 4. Axes are described in the manuscript.

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Additional file 3:

MVA plots: between plate cell line replicates. Pre-normalization MVA plots for 200 ng between SAM cell line technical replicates corresponding to panel C of Figures 3 and 4. Axes are described in the manuscript.

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Additional file 4:

MVA plots: between plate patient replicates. Pre-normalization MVA plots for 200 ng between SAM patient technical replicates for 200 ng of extraction 1 corresponding to panel D of Figures 3 and 4. Axes are described in the manuscript.

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Additional file 5:

MVA plots: between extractions. Pre-normalization MVA plots for 200 ng between extraction patient technical replicates for 200 ng corresponding to panel E of Figures 3 and 4. Axes are described in the manuscript.

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Additional file 6:

MVA plots: between dilutions. Pre-normalization MVA plots for patient samples from extraction 1 comparing 25, 100, 400, 800 ng to 200 ng for two patients corresponding to panel F of Figures 3 and 4. Axes are described in the manuscript.

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Additional file 7:

Pre-normalization clustering dendrogram, plate 1. Pre-normalization dendrogram depicting the results of clustering performed on patient samples on plate 1. Sample IDs are of the form Tdilution.ptID.extraction.replicate. For example, T200.133.1a.1 represents the 200 ng dilution for patient 133 from extraction 1, replicate 1.

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Additional file 8:

Post-normalization clustering dendrogram, plate 1. Post-normalization dendrogram depicting the results of clustering performed on patient samples on plate 1. Sample IDs are as described for Additional file 7.

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Additional file 9:

Pre-normalization clustering dendrogram, plate 2. Pre-normalization dendrogram depicting the results of clustering performed on patient samples on plate 2. Sample IDs are as described for Additional file 7.

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Additional file 10:

Post-normalization clustering dendrogram, plate 2. Post-normalization dendrogram depicting the results of clustering performed on patient samples on plate 2. Sample IDs are as described for Additional file 7.

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Additional file 11:

Venn diagrams of signal detection between replicates. Venn diagrams showing overlap in detection calls between each dilution and the 200 ng replicate 1 for both patients with dilution replicates on SAM 2. Each box represents comparison of one dilution versus the 200 ng replicate 1 sample, where the dilution is labeled on the tops of circles within a box. The numbers inside the circles indicate the number of probes detected in the 200 dilution, both dilutions, or the comparison using the p = 0.01 cut-off to determine detection. The numbers in the bottom right of each box indicate the number of probes not detected in either dilution. For example, for patient 45 comparing 200 ng versus 25 ng, 388 probes were detected in both dilutions, 73 or 16 probes were detected in only the 200 ng or 25 ng dilution, respectively, and 258 were not detected in either dilution.

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