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Series GSE1722 Query DataSets for GSE1722
Status Public on Mar 01, 2005
Title Cross-platform reproducibility of oligonucleotide microarray expression profiles
Organism Homo sapiens
Experiment type Expression profiling by array
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
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
Phone +49 6221 424672
Fax +49 6221 424639
Organization name German Cancer Research Center (DKFZ)
Department Molecular Biology (B060)
Lab Expression Profiling Facility
Street address Technologiepark III, Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platforms (2)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
GPL1384 DKFZ Operon 27k long oligonucleotide array
Samples (24)
GSM29702 Affy 1606PT
GSM29703 Affy 1607N
GSM29704 Affy 1713PT
BioProject PRJNA90385

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE1722_RAW.tar 1.4 Gb (http)(custom) TAR (of CEL, TIFF)

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