{"owner": "ArrayExpress Uploader", "pop_total": 0, "species": "mouse", "factors": [{"GSM552243": {"TIME": "24h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "25\u00c2\u00b5M"}}, {"GSM552243": {"TIME": "24h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "25\u00c2\u00b5M"}}, {"GSM552243": {"TIME": "24h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "25\u00c2\u00b5M"}}, {"GSM552246": {"TIME": "120h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "25\u00c2\u00b5M"}}, {"GSM552246": {"TIME": "120h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "25\u00c2\u00b5M"}}, {"GSM552246": {"TIME": "120h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "25\u00c2\u00b5M"}}, {"GSM552249": {"TIME": "24h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.5\u00c2\u00b5M"}}, {"GSM552249": {"TIME": "24h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.5\u00c2\u00b5M"}}, {"GSM552249": {"TIME": "24h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.5\u00c2\u00b5M"}}, {"GSM552252": {"TIME": "120h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.5\u00c2\u00b5M"}}, {"GSM552252": {"TIME": "120h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.5\u00c2\u00b5M"}}, {"GSM552252": {"TIME": "120h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.5\u00c2\u00b5M"}}, {"GSM552255": {"TIME": "24h", "TREATMENT": "control of the first experimental approach", "DOSE": "not specified"}}, {"GSM552255": {"TIME": "24h", "TREATMENT": "control of the first experimental approach", "DOSE": "not specified"}}, {"GSM552255": {"TIME": "24h", "TREATMENT": "control of the first experimental approach", "DOSE": "not specified"}}, {"GSM552258": {"TIME": "120h", "TREATMENT": "control of the first experimental approach", "DOSE": "not specified"}}, {"GSM552258": {"TIME": "120h", "TREATMENT": "control of the first experimental approach", "DOSE": "not specified"}}, {"GSM552258": {"TIME": "120h", "TREATMENT": "control of the first experimental approach", "DOSE": "not specified"}}, {"GSM55226": {"TIME": "24h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "50\u00c2\u00b5M"}}, {"GSM55226": {"TIME": "24h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "50\u00c2\u00b5M"}}, {"GSM55226": {"TIME": "24h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "50\u00c2\u00b5M"}}, {"GSM552264": {"TIME": "120h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "50\u00c2\u00b5M"}}, {"GSM552264": {"TIME": "120h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "50\u00c2\u00b5M"}}, {"GSM552264": {"TIME": "120h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "50\u00c2\u00b5M"}}, {"GSM552267": {"TIME": "24h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "2\u00c2\u00b5M"}}, {"GSM552267": {"TIME": "24h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "2\u00c2\u00b5M"}}, {"GSM552267": {"TIME": "24h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "2\u00c2\u00b5M"}}, {"GSM552270": {"TIME": "120h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "2\u00c2\u00b5M"}}, {"GSM552270": {"TIME": "120h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "2\u00c2\u00b5M"}}, {"GSM552270": {"TIME": "120h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "2\u00c2\u00b5M"}}, {"GSM552273": {"TIME": "24h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "10\u00c2\u00b5M"}}, {"GSM552273": {"TIME": "24h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "10\u00c2\u00b5M"}}, {"GSM552273": {"TIME": "24h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "10\u00c2\u00b5M"}}, {"GSM552276": {"TIME": "120h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "10\u00c2\u00b5M"}}, {"GSM552276": {"TIME": "120h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "10\u00c2\u00b5M"}}, {"GSM552276": {"TIME": "120h", "TREATMENT": "2-Acetylaminoflourene (AAF)", "DOSE": "10\u00c2\u00b5M"}}, {"GSM552279": {"TIME": "24h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "1.5\u00c2\u00b5M"}}, {"GSM552279": {"TIME": "24h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "1.5\u00c2\u00b5M"}}, {"GSM552279": {"TIME": "24h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "1.5\u00c2\u00b5M"}}, {"GSM552282": {"TIME": "120h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.1\u00c2\u00b5M"}}, {"GSM552282": {"TIME": "120h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.1\u00c2\u00b5M"}}, {"GSM552282": {"TIME": "120h", "TREATMENT": "benzo(a)pyrene (BaP)", "DOSE": "0.1\u00c2\u00b5M"}}, {"GSM552285": {"TIME": "24h", "TREATMENT": "E2 = control of the second experimental approach", "DOSE": "not specified"}}, {"GSM552285": {"TIME": "24h", "TREATMENT": "E2 = control of the second experimental approach", "DOSE": "not specified"}}, {"GSM552285": {"TIME": "24h", "TREATMENT": "E2 = control of the second experimental approach", "DOSE": "not specified"}}, {"GSM552288": {"TIME": "120h", "TREATMENT": "E2 = control of the second experimental approach", "DOSE": "not specified"}}, {"GSM552288": {"TIME": "120h", "TREATMENT": "E2 = control of the second experimental approach", "DOSE": "not specified"}}, {"GSM552288": {"TIME": "120h", "TREATMENT": "E2 = control of the second experimental approach", "DOSE": "not specified"}}, {"GSM55229": {"TIME": "24h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "700\u00c2\u00b5M"}}, {"GSM55229": {"TIME": "24h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "700\u00c2\u00b5M"}}, {"GSM55229": {"TIME": "24h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "700\u00c2\u00b5M"}}, {"GSM552294": {"TIME": "120h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "0.2\u00c2\u00b5M"}}, {"GSM552294": {"TIME": "120h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "0.2\u00c2\u00b5M"}}, {"GSM552294": {"TIME": "120h", "TREATMENT": "2, 4-diaminotoluene (DAT)", "DOSE": "0.2\u00c2\u00b5M"}}, {"GSM552297": {"TIME": "24h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "20\u00c2\u00b5M"}}, {"GSM552297": {"TIME": "24h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "20\u00c2\u00b5M"}}, {"GSM552297": {"TIME": "24h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "20\u00c2\u00b5M"}}, {"GSM552300": {"TIME": "120h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "0.1\u00c2\u00b5M"}}, {"GSM552300": {"TIME": "120h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "0.1\u00c2\u00b5M"}}, {"GSM552300": {"TIME": "120h", "TREATMENT": "3-methycholanthrene (MCA)", "DOSE": "0.1\u00c2\u00b5M"}}], "id": 6117, "ownerprofile_id": "arrayexpress_sid", "platform": 6, "summary_wrapped": "Background: Information on the carcinogenic potential of chemicals is only availably for High Production Volume products. There is...", "pubmed_id": 20713471, "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 3, "sample_count": 60, "tags": ["cancer", "cell", "dish", "genome", "volume"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_id_plat": "E-GEOD-22180_A-AFFY-45", "slug": "in-vitro-carcinogenicity-testing-with-balbc-3t3-ce", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22180", "geo_gds_id": "", "name": "In vitro carcinogenicity testing with Balb/c 3T3 Cells treated with various chemical carcinogens", "created": "Nov.11, 2014", "summary": "Background: Information on the carcinogenic potential of chemicals is only availably for High Production Volume products. There is however, a pressing need for alternative methods allowing for the chronic toxicity of substances, including carcinogenicity, to be detected earlier and more reliably. Here we applied advanced genomics to a cellular transformation assay to identify gene signatures useful for the prediction of risk for carcinogenicity.  Methods: Genome wide gene expression analysis and qRT-PCR were applied to untransformed and transformed Balb/c 3T3 cells that exposed to 2, 4-diaminotoluene (DAT), benzo(a)pyrene (BaP), 2-Acetylaminoflourene (AAF) and 3-methycholanthrene (MCA) for 24h and 120h, at different concentrations, respectively. Furthermore, various bioinformatics tools were used to identify gene signatures predicting for the carcinogenic risk.  Results: Bioinformatics analysis revealed distinct datasets for the individual chemicals tested while the number of significantly regulated genes increased with ascending treatment concentration of the cell cultures. Filtering of the data revealed a common gene signature that comprised of 13 genes whose regulation in cancer tissue has already been established. Strikingly, this gene signature was already identified prior to cell transformation therefore confirming the predictive power of this gene signature in identifying carcinogenic risks of chemicals. Comparison of fold changes determined by microarray analysis and qRT-PCR were in good agreement.   Conclusion: Our data describes selective and commonly regulated carcinogenic pathways   observed in an easy to use in vitro carcinogenicity assay. Here we defined a set of genes which can serve as a simply assay to predict the risk for carcinogenicity by use of an alternative in vitro testing strategy. 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 (0.5\u00b5M BaP, 50\u00b5M DAT, 25\u00b5M AAF and 2\u00b5M 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 \u00b5M BaP to 700 \u00b5M DAT for 24h of treatment, and from 0.1 \u00b5M BaP or MCA to 10\u00b5M AAF for 120h of treatment. Balb/c 3T3 cells treated with 0.75% DMSO alone were kept as controls. Each experiment was run in triplicate.", "geo_gse_id": "E-GEOD-22180", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22180/samples/"}