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Open AccessResearch article

Validation of oligoarrays for quantitative exploration of the transcriptome

Vigdis Nygaard* 1 email, Fang Liu* 1,2 email, Marit Holden3 email, Winston P Kuo4,5,6 email, Jeff Trimarchi7 email, Lucila Ohno-Machado6 email, Connie L Cepko7,8 email, Arnoldo Frigessi3,9 email, Ingrid K Glad10 email, Mark A van de Wiel11,12 email, Eivind Hovig1,13 email and Heidi Lyng14 email

1Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, Oslo, Norway

2PubGene AS, Vinderen, Oslo, Norway

3Norwegian Computing Center, Oslo, Norway

4Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA

5Laboratory for Innovative Translational Technologies, Harvard School of Dental Medicine, Boston, MA, USA

6Decision Systems Group, Brigham and Women's Hospital, Boston, MA, USA

7Department of Genetics, Harvard Medical School, Boston, MA, USA

8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA

9Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Norway

10Department of Mathematics, University of Oslo, Norway

11Department of Mathematics, Vrije Universiteit Amsterdam, The Netherlands

12Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands

13Department of Medical Informatics, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, Oslo, Norway

14Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, Norway

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:258doi:10.1186/1471-2164-9-258

Published: 30 May 2008

Additional files

Additional file 1:

Transcript data of genes in common for oligoarrays, MPSS, and SAGE. The file lists transcript data obtained with oligoarrays (number of transcripts per μg total RNA and number of transcripts per cell), MPSS (tags per million and tags per cell) and SAGE (tags per million and tags per cell) for the overlapping genes.

Format: XLS Size: 215KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

QRT-PCR primer sequences, The file lists the forward and reverse primer sequences and amplicon sequences for the qRT-PCR analyses.

Format: XLS Size: 22KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

PCR amplification efficiency of selected genes. The file lists the slope and standard deviation of linear curves fitted to plots of cycle threshold (Ct) versus primer dilution for the genes subjected to qRT-PCR analysis.

Format: XLS Size: 23KB Download file

This file can be viewed with: Microsoft Excel Viewer


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