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E-GEOD-6274 - Transcription profiling of human HFF2 and Colo320DM cells GAPF profiles

Status
Submitted on 14 November 2006, released on 14 June 2008, last updated on 27 March 2012
Organism
Homo sapiens
Samples (6)
Array (1)
Protocols (4)
Description
Amplification of large chromosomal regions (gene amplification) is a common somatic alteration in human cancer cells and often is associated with advanced disease. A critical event initiating gene amplification is a DNA double strand break (DSB), which is immediately followed by the formation of a large DNA palindrome. Large DNA palindromes are frequent and non-randomly distributed in the genomes of cancer cells and facilitate further increase in copy number. Although the importance of the formation of large DNA palindromes as a very early event in gene amplification is widely recognized, it is not known 1) how a DSB is resolved to form a large DNA palindrome; and 2) whether any local DNA structure determines the location of large DNA palindromes. We show here that intra-strand annealing following a DNA double-strand break leads to the formation of large DNA palindromes and that DNA inverted repeats in the genome determines the efficiency of this event. Furthermore, in human Colo320DM cancer cells, a DNA inverted repeat in the genome marks the border between amplified and non-amplified DNA. Therefore, an early step of gene amplification is a regulated process that is facilitated by DNA inverted repeats in the genome. Experiment Overall Design: Genomic DNA samples from HFF2 and Colo320DM cells were collected and taken through the GAPF procedure. Their GAPF profiles were analyzed using Affymetrix HGU 133A arrays, and the differentially hybridized genes were determined to be significant according to a FDR<0.05
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Intrastrand annealing leads to the formation of a large DNA palindrome and determines the boundaries of genomic amplification in human cancer. Hisashi Tanaka, Yi Cao, Donald A Bergstrom, Charles Kooperberg, Stephen J Tapscott, Meng-Chao Yao. Mol Cell Biol 27(6):1993-2002 (2007)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-6274.idf.txt
Sample and data relationshipE-GEOD-6274.sdrf.txt
Raw data (1)E-GEOD-6274.raw.1.zip
Processed data (1)E-GEOD-6274.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-6274.eSet.r
Links