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| Status |
Public on Mar 01, 2005 |
| Title |
Cross-platform reproducibility of oligonucleotide microarray expression profiles |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Both spotted long oligonucleotide arrays (GPL1384) and Affymetrix GeneChip arrays (GPL96) were used to analyze gene expression in six human head and neck squamous cell carinoma samples versus control samples or lymph node metastases of the same patients. Hybridizations of HG-U133A GeneChip arrays were performed using standard Affymetrix protocols and equipment. Before hybridization on DKFZ Operon 27k long oligonucleotide arrays, 2 µg RNA were amplified by one round of linear isothermal RNA amplification, followed by Cy-dUTP incorporation using Klenow fragment. Hybridizations were performed for 16 h at 42 °C in a GeneTAC Hybridization Station (Genomic Solutions) using UltraHyb hybridization buffer (Ambion). Hybridized microarrays were scanned at 5 µm resolution on a GenePix 4000B microarray scanner (Axon Instruments). Raw signal intensities from both platforms were normalized applying variance stabilization (W. Huber et al., Bioinformatics 18 Suppl 1, 2002). Expression ratios were compared for those genes represented in both array platforms.
Keywords: parallel sample
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| Contributor(s) |
Schlingemann J, Habtemichael N, Ittrich C, Benner A, Hahn M, Stauber R, Lichter P, Kramer H |
| Citation(s) |
16205657 |
| |
| Submission date |
Sep 01, 2004 |
| Last update date |
Aug 10, 2018 |
| Contact name |
Joerg Schlingemann |
| E-mail(s) |
[email protected]
|
| Phone |
+49 6221 424672
|
| Fax |
+49 6221 424639
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| URL |
http://www.dkfz-heidelberg.de/kompl_genome/index.html
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| Organization name |
German Cancer Research Center (DKFZ)
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| Department |
Molecular Biology (B060)
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| Lab |
Expression Profiling Facility
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| Street address |
Technologiepark III, Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platforms (2) |
| GPL96 |
[HG-U133A] Affymetrix Human Genome U133A Array |
| GPL1384 |
DKFZ Operon 27k long oligonucleotide array |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA90385 |
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