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Series GSE11225 Query DataSets for GSE11225
Status Public on Apr 22, 2008
Title Array-comparative genomic hybridization by using DualChip® human cancer 1.1 arrays
Organism Homo sapiens
Experiment type Genome variation profiling by array
Genome variation profiling by genome tiling array
Summary Tumors often harbor several genetic aberrations at both RNA and DNA level. Integration of expression data with copy number changes represents a powerful strategy to investigate genes involved in tumorigenesis. Here we describe a fluorescent array-based Comparative Genomic Hybridization protocol to be used on a commercial microarray platform optimized to detect cancer-related gene expression. This method will be valuable to use a single low-density array platform monitoring gene expression and copy number assessment in parallel.
Keywords: Comparative genomic hybridization, neuroblastoma
 
Overall design Here we describe a fluorescent array-based Comparative Genomic Hybridization (aCGH) protocol to be used on DualChip® (Eppendorf, Hamburg, Germany) arrays, in view of an application of cancer-specific DualChip® platforms for both gene expression profiling and copy number assessment.
Since we previously analyzed #501 and #2270 neuroblastoma samples by Agilent Human Genome CGH 44A microarrays (Scaruffi, P. Coco, S., Cifuentes, F., Albino, D., Nair, M., Defferrari, R., Mazzocco, K., and G.P. Tonini. 2007. Identification and characterization of DNA imbalances in neuroblastoma by high-resolution oligonucleotide array comparative genomic hybridization. Cancer Genetics and Cytogenetics. 177(1): 20-29) and all 294 genes contained in DualChip® human cancer 1.1 arrays were present also in Agilent arrays, it has been possible to compare results obtained by the two different platforms. We assumed aCGH performed by Agilent slides as reference method to assess gene gains and losses in neuroblastoma samples. This approach allowed us to select 120 genes printed on DualChip® arrays as invariant genes (ABI2, ADAM9, ANGPT1, AREG, BAK1, BIK, BARD1, BCL2A1, BCL2L2, BMP1, CASP3, CASP8, CDH12, CFLAR, CTNNA1, CD34, CLK1, CGRRF1, COL6A1, CSF1R, CSPG2, CTGF, CXCL9, CCNA2, CCNB1, CCNG1, CCNH, CDKN1A, CDKN1C, CDKN2A, CDKN2B, CDKL1, DSP, E2F3, E2F5, EFNA1, EGF, EGR1, FASTK, FGF1, FGF2, FGFR1, FGR, FN1, GAS1, HGFAC, HMMR, IGF1R, IGFBP2, IK, IFNAR1, IFNGR1, ILK, IRF1, ITGA1, ITGA4, IL10, IL13, IL15, IL1A, IL2, IL3, IL4, IL5, IL6R, IL8, KDR, KISS1, LIF, MIF, MMP11, MMP14,
MDH1, MAP2K1, MAP2K5, MAPK10, MAPK14, MCL1, NF2, NID1, NINJ1, NRG1, NTRK1, PGF, PDGFB, PDGFRA, PLAT, PLG, PDCD2, PPBP, PRODH, PTGES, PCDH1, PTK2, PURA, QSCN6, RIPK1, RRM1, ARHGDIA, SFRP2, SOD1, STAT1, TEK, TERT, THBS1, TIAM1, TNC, TANK, TGFA, TGFB2, XRCC6, TGFB3, TGFBR1, TMED10, TPBG, TYRO3, ERBB4, FLT4, FOS, VIL2).


 
Contributor(s) Scaruffi P, Moretti S, Cremonesi C, Bonassi S, Tonini G
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 21, 2008
Last update date Dec 06, 2012
Contact name PAOLA SCARUFFI
E-mail(s) paola.scaruffi@hsanmartino.it
Organization name "San Martino" Hospital
Lab Center of Physiopathology of Human Reproduction
Street address LARGO R. BENZI, 10
City Genova
State/province GE
ZIP/Postal code 16132
Country Italy
 
Platforms (2)
GPL2873 Agilent-012750 Human Genome CGH Microarray 44A (Feature number version)
GPL6745 Eppendorf DualChip Human Cancer v1.1
Samples (4)
GSM281935 501_Dualchip
GSM282642 2270_Dualchip
GSM283057 501_Agilent
Relations
BioProject PRJNA106835

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

Supplementary file Size Download File type/resource
GSE11225_RAW.tar 19.9 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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