Open Access Research article

Validation of oligoarrays for quantitative exploration of the transcriptome

Vigdis Nygaard1†, Fang Liu1,2†, Marit Holden3, Winston P Kuo4,5,6, Jeff Trimarchi7, Lucila Ohno-Machado6, Connie L Cepko7,8, Arnoldo Frigessi3,9, Ingrid K Glad10, Mark A Wiel11,12, Eivind Hovig1,13 and Heidi Lyng14*

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

2 PubGene AS, Vinderen, Oslo, Norway

3 Norwegian Computing Center, Oslo, Norway

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

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

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

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

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

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

10 Department of Mathematics, University of Oslo, Norway

11 Department of Mathematics, Vrije Universiteit Amsterdam, The Netherlands

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

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

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

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BMC Genomics 2008, 9:258 doi: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

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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

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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

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Open Data