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Sample GSM357366 Query DataSets for GSM357366
Status Public on Apr 01, 2009
Title NDMA biological replicate 3
Sample type RNA
 
Channel 1
Source name Control for NDMA 24h
Organism Homo sapiens
Characteristics Caco-2 (Human colonic adenocarcinoma cells)
Treatment protocol Caco-2 cells were treated for 24 hours with one of the following six NOC: MNNG (1μM), MNU (1mM), NDEA (50mM), NDMA (100mM), NPIP (40mM) and NPYR (100mM)
Growth protocol Caco-2 cell cultures were transferred weekly by trypsinization and incubated at 37 ºC in a humidified incubator containing 5% CO2
Extracted molecule total RNA
Extraction protocol RNA was isolated from TRIzol® suspended cells according to the manufacturer’s protocol with minor modifications, followed by a clean up, using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) with DNase treatment.
Label Cy3
Label protocol The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.
 
Channel 2
Source name NDMA 100mM 24h
Organism Homo sapiens
Characteristics Caco-2 (Human colonic adenocarcinoma cells)
Treatment protocol Caco-2 cells were treated for 24 hours with one of the following six NOC: MNNG (1μM), MNU (1mM), NDEA (50mM), NDMA (100mM), NPIP (40mM) and NPYR (100mM)
Growth protocol Caco-2 cell cultures were transferred weekly by trypsinization and incubated at 37 ºC in a humidified incubator containing 5% CO2
Extracted molecule total RNA
Extraction protocol RNA was isolated from TRIzol® suspended cells according to the manufacturer’s protocol with minor modifications, followed by a clean up, using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) with DNase treatment.
Label Cy5
Label protocol The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.
 
 
Hybridization protocol Hybridization according to Agilent instructions.
Scan protocol Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.
Description Biological replicate 3 of 4
Data processing Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of test compound versus respective vehicle control.
 
Submission date Jan 05, 2009
Last update date Jan 05, 2009
Contact name Dennie Hebels
E-mail(s) d.hebels@maastrichtuniversity.nl
Phone 0031-43-3881088
Fax 0031-43-3884146
URL http://www.grat.nl
Organization name Maastricht University
Department Health Risk Analysis and Toxicology
Street address Universiteitssingel 50
City Maastricht
ZIP/Postal code 6200MD
Country Netherlands
 
Platform ID GPL6480
Series (1)
GSE14284 Molecular signatures of N-nitroso compounds in Caco-2 cells: implications for colon carcinogenesis

Data table header descriptions
ID_REF
VALUE Background corrected, LOWESS normalized log2 ratio (test compound/control)

Data table
ID_REF VALUE
A_23_P100001 -0.4476
A_23_P100011 -0.3211
A_23_P100022 1.1035
A_23_P100056 -0.9248
A_23_P100074 0.0245
A_23_P100092 0.8438
A_23_P100103 -0.0234
A_23_P100111 -0.5964
A_23_P100127 0.1019
A_23_P100133 0.0540
A_23_P100141 -0.1665
A_23_P100156 0.2555
A_23_P100177 -0.7965
A_23_P100189 0.3983
A_23_P100196 -0.4427
A_23_P100203 -0.5360
A_23_P100220 -0.1387
A_23_P100240 -1.2485
A_23_P10025 2.5537
A_23_P100263 -0.0228

Total number of rows: 41000

Table truncated, full table size 740 Kbytes.




Supplementary file Size Download File type/resource
GSM357366_Cy3.txt.gz 4.3 Mb (ftp)(http) TXT
GSM357366_Cy5.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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