Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Expression microarray analysis of acquired gemcitabine resistance


ABSTRACT: This series repressents the data set from the paper "Expression microarray analysis and oligo array CGH of aquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations". Biological material: One solid mouse tumor "Colon 26A" was routinely maintained by successive transplantation. A subset of mice with this tumor was treated at the maximum tolerable dosage of Gemcitabine and successively transplanted 5 times and similarly treated. The last passage was completly resistant and designated, "Colon 26G". Expression array: Total RNA was isolated from frozen mouse tumors using Tryzol. Single stranded cDNA was synthetized from 30 mg of total RNA by reverse transcription using aminoallyl labeled dUTP (Ambion). Labelling was performed according to the aminoallyl labeling protocol. Briefly, cDNA was incubated at room temperature for 1 h with fluorolink monofunctional cy5 or cy3 (Amersham) followed by 15 min 4 M hydroxylamine treatment. Uncoupled dyes were removed using Qiaquick PCR purification columns (Qiagen) and mixed with 12 mg poly(dA) (Amersham), 60 mg yeast tRNA (Sigma) and 24 mg Cot-1 DNA (Invitroen). The probe was dissolved in 127 ml hybridization mixture containing 46% formamide, 9.5% dextran sulfate, 2x SSC and 0.2% SDS. The probe was heated to 70°C for 10 min and annealed at 37°C for 1 h. Slides were hybridized for 14 h at 37°C over-night (HyArray 12™, Perkin Elmer). After hybridization the slides were washed in the HybArray 12™ with 50% formamide, 2x SSC, pH 7 at 35°C for 15 min, followed b PI buffer (0.1 M sodium phosphate, 0.1% Igepal Ca630, pH 8) at room temperature and 3 washes of 0.2x SSC, 0.1x SSC and 0.01x SSC at room temperature followed by centrifugation. Arrays were scanned using a laser scanner (ScanArray Express, Perkin Elmer) and analysed using ImaGene version 5.6. Cy5 cy3 ratios are calculating by taking the log2 of the signal mean of each spot minus the median background mean of all spots on the array. This is followed by a standard normalization for spot intensity and calculation of the ratios.

ORGANISM(S): Mus musculus

SUBMITTER: Paul van den IJssel 

PROVIDER: E-GEOD-2352 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

Expression microarray analysis and oligo array comparative genomic hybridization of acquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations.

van de Wiel Mark A MA   Costa Jose L JL   Smid Kees K   Oudejans Cees B M CB   Bergman Andries M AM   Meijer Gerrit A GA   Peters Godefridus J GJ   Ylstra Bauke B  

Cancer research 20051101 22


Gemcitabine is a commonly used therapy for many solid tumors. Acquired resistance to this nucleoside analogue, however, diminishes the long-term effectiveness in a majority of patients. To better define the molecular background of gemcitabine resistance, a mouse colon tumor was selected during successive rounds of transplantation with continued treatment of gemcitabine. Expression microarray analysis was applied to determine which genes are consistently and highly overexpressed or underexpressed  ...[more]

Similar Datasets

2010-06-11 | E-GEOD-2064 | biostudies-arrayexpress
2010-06-11 | E-GEOD-1887 | biostudies-arrayexpress
2009-03-25 | E-GEOD-15136 | biostudies-arrayexpress
2011-10-13 | E-GEOD-18441 | biostudies-arrayexpress
2009-02-15 | E-GEOD-14240 | biostudies-arrayexpress
2010-06-24 | E-GEOD-14589 | biostudies-arrayexpress
2010-06-05 | E-GEOD-335 | biostudies-arrayexpress
2010-05-18 | E-GEOD-14207 | biostudies-arrayexpress
2014-11-18 | PXD001354 | Pride
2010-06-05 | E-GEOD-2454 | biostudies-arrayexpress