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Sample GSM552246 Query DataSets for GSM552246
Status Public on Oct 02, 2010
Title AAF_25µM_120h_Replicate1
Sample type RNA
 
Source name embryonic mouse fibroblasts Balb/c 3T3 cell line
Organism Mus musculus
Characteristics strain: BALB/c
cell line: 3T3 cell line
treatment: 2-Acetylaminoflourene (AAF)
dose: 25µM
time: 120h
Treatment protocol Balb/c 3T3 cells were seeded at 200 cells in each 60 x 15 mm culture dish with 4 ml M10F, using six culture dishes for every treatment. When cells reached a confluence of 60-65%, the culture medium was removed and replaced with fresh medium containing all tested chemicals at a specific concentration and two time points (24 and 120h). First we treated the cells both 24h and 120h with concentrations reported in the literature (0.5µM BaP, 50µM DAT, 25µM AAF and 2µM MCA). In a second approach IC20 concentrations were investigated for each chemical at both time points. The concentrations determined for IC20 ranged from 1.5 µM BaP to 700 µM DAT for 24h of treatment, and from 0.1 µM BaP or MCA to 10µM AAF for 120h of treatment. Balb/c 3T3 cells treated with 0.75% DMSO alone were kept as controls.
Growth protocol The Balb/c 3T3 cell line was obtained from Cytotest Cell Research GmbH (RCC), Roßdorf, Germany. Cells were harvested and used within 9-10 passages to perform the experiments. Cells were cultured with M10F containing MEM (minimum essential medium) + 10% FBS and incubated at 37 °C and 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA-extraction was performed with the RNeasy Mini Kit (RNeasy MidiKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).
Label biotin
Label protocol Total RNA (5µg) was used to generate biotin-labeled cRNA (10 µg) by means of GeneChip® One-Cycle cDNA Synthesis Kit and GeneChip® IVT Labeling Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a Bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).
 
Hybridization protocol Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome - 430 2.0 arrays covering approximately 36,000 full-length mouse gene transcripts and stained according to the manufacturer's instructions.
Scan protocol The arrays were scanned using the GeneChip® Scanner 3000.
Description n/a
Data processing Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same (GCOS). The Scale factor (SF) was according to the Affymetrix recommended setting SF=1 and the TGT value was 500 and were used to generate a microarray quality control and data report. A T-test analysis was performed using Data Mining Tool (DMT) 3.0 from Affymetrix. A stringent comparison between normal and tumoral tissues was performed according to the consistency of gene expression changes. A t-test and a ranking analysis with up- and down-regulated genes were performed and only genes that exhibit a 100% concordance in the change direction with a p-value < 0.05 (t-test) and a fold change (FC) *2/FC*-2 were reported.
 
Submission date Jun 07, 2010
Last update date Oct 02, 2010
Contact name Astrid Rohrbeck
E-mail(s) rohrbeck.astrid@mh-hannover.de
Phone 0511-5322807
Organization name Medizinische Hochschule Hannover
Department Department of Toxicology
Street address Carl-Neuberg-Straße 1
City Hannover
State/province Niedersachsen
ZIP/Postal code 30625
Country Germany
 
Platform ID GPL1261
Series (1)
GSE22180 In vitro carcinogenicity testing with Balb/c 3T3 Cells treated with various chemical carcinogens

Data table header descriptions
ID_REF
VALUE GCOS signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 183.66
AFFX-BioB-M_at 211.924
AFFX-BioB-3_at 181.783
AFFX-BioC-5_at 419.813
AFFX-BioC-3_at 506.574
AFFX-BioDn-5_at 1148.97
AFFX-BioDn-3_at 1593.04
AFFX-CreX-5_at 5728.22
AFFX-CreX-3_at 6071.42
AFFX-DapX-5_at 3.59806
AFFX-DapX-M_at 8.75085
AFFX-DapX-3_at 5.50807
AFFX-LysX-5_at 1.27008
AFFX-LysX-M_at 14.7109
AFFX-LysX-3_at 11.6705
AFFX-PheX-5_at 6.48377
AFFX-PheX-M_at 17.1354
AFFX-PheX-3_at 22.3515
AFFX-ThrX-5_at 5.42012
AFFX-ThrX-M_at 10.3235

Total number of rows: 45101

Table truncated, full table size 852 Kbytes.




Supplementary file Size Download File type/resource
GSM552246.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM552246.chp.gz 326.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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