Optimization of cDNA microarrays procedures using criteria that do not rely on external standards

doi:10.1186/1471-2164-8-377

BMC Genomics

Volume 8

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Doseth B
Bergum H
Beisvag V
Lægreid A

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Methodology article

Optimization of cDNA microarrays procedures using criteria that do not rely on external standards

Torunn Bruland¹^* , Endre Anderssen¹^,2^* , Berit Doseth¹ , Hallgeir Bergum² , Vidar Beisvag¹^,2 and Astrid Lægreid¹^,2

¹Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology (NTNU), N-7489 Trondheim, Norway.

²NTNU Microarray Core Facility, Norwegian University of Science and Technology (NTNU), N-7489 Trondheim, Norway.

author email corresponding author email* Contributed equally

BMC Genomics 2007, 8:377doi:10.1186/1471-2164-8-377


Published:	18 October 2007

Additional files

Additional file 1:

Table S1. Number of differentially expressed genes under different blocking, background correction and levels of filtration. The file shows all combinations of blocking, background correction and levels of filtration together with the estimated numbers of differentially expressed genes with the different combinations.

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Additional file 2:

Table S2. Level of concordance of biological themes represented in the gene list generated with different background correction methods. The file shows all GO terms at hierarchy level 1–3 which was associated with five or more genes(n = 64).

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Additional file 3:

Figure S1. Validation of differentially expressed genes by SYBR green-based quantitative real-time PCR. The figure shows fold changes for a few selected genes on the microarry platforms and the correspondence with relative gene expression data from qRT-PCR assays.

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Additional file 4:

Cross platform microarray analysis (Table S3a) and SYBR green-based quantitative real-time PCR (Table S3b). The file shows log2 ratio differences and fold ratios for a few selected genes on the microarray platforms (Table S3a) compared to ΔΔCt values and calculated fold change values from validation by qRT-PCR (Table S3b).

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Additional file 5:

PCR primers (Table S4) and qRT-PCR protocol. The file gives information about the PCR primers and the qRT-PCR protocol used in the study.

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