GEO DataSets

(Submitter supplied) For assessing the cancer-causing potential for humans of a chemical compound, the conventional approach is the use of the 2-year rodent carcinogenicity bioassay, thus alternatives such as in vitro toxicogenomics are highly desired. In the present study, the transcriptomics responses following exposure to genotoxic (GTX) and non-genotoxic (NGTX) hepatocarcinogens and non-carcinogens (NC) in five liver-based in vitro models, namely conventional and epigenetically-stabilized cultures of primary rat hepatocytes, the human hepatoma-derived HepaRG and HepG2 cell lines and the human embryonic stem cell-derived hepatocyte-like cells hES-Heps are examined and compared.

Organism:

Rattus norvegicus; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL15933 GPL13916

548 Samples

Download data: CEL

(Submitter supplied) At present, substantial efforts are focused on the development of in vitro assays coupled with ”omics” technologies for the identification of carcinogenic substances as an alternative to the classical 2-year rodent carcinogenicity bioassay. A prerequisite for the eventual regulatory acceptance of such assays, however, is the in vivo relevance of the observed in vitro findings.

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

72 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Rattus norvegicus; Mus musculus

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL18609 GPL18615

120 Samples

Download data: CEL, GPR, TXT

(Submitter supplied) The study investigated differential gene expression in primary mouse hepatocyte mRNA following 24 and 48 hours of exposure to aflatoxin B1, cisplatin, benzo(a)pyrene, 2,3,7,8-tetrachloordibenzo-p-dioxine, cyclosporin A or Wy-14,643 or their responsive solvent. Three (four for Wy-14,643) biological replicates per compound/solvent.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL18615

60 Samples

Download data: CEL

(Submitter supplied) The study investigated differential miRNA changes in primary mouse hepatocyte following 24 and 48 hours of exposure to aflatoxin B1, cisplatin, benzo(a)pyrene, 2,3,7,8-tetrachloordibenzo-p-dioxine, cyclosporin A or Wy-14,643 or their responsive solvent. Three (four for Wy-14,643) biological replicates per compound/solvent.

Organism:

Homo sapiens; Rattus norvegicus; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL18609

60 Samples

Download data: GPR, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL15592 GPL11084

30 Samples

Download data: CEL

(Submitter supplied) The transcriptomic changes induced in primary mouse hepatocytes (C57BL/6 ) by 7µM of cisplatin after treatment for 24 and 48h

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL15592

12 Samples

Download data: CEL

(Submitter supplied) The transcriptomic changes induced in the human liver cell line HepG2 by 7µM of cisplatin after treatment for 12, 24 and 48h

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11084

18 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL18609 GPL18615

340 Samples

Download data: CEL, GPR, TXT

(Submitter supplied) The well-defined battery of in vitro systems applied within chemical cancer risk assessment is often characterised by a high false-positive rate, thus repeatedly failing to correctly predict the in vivo genotoxic and carcinogenic properties of test compounds. Toxicogenomics, i.e. mRNA-profiling, has been proven successful in improving the prediction of genotoxicity in vivo and the understanding of underlying mechanisms. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL18615

184 Samples

Download data: CEL

(Submitter supplied) The well-defined battery of in vitro systems applied within chemical cancer risk assessment is often characterised by a high false-positive rate, thus repeatedly failing to correctly predict the in vivo genotoxic and carcinogenic properties of test compounds. Toxicogenomics, i.e. mRNA-profiling, has been proven successful in improving the prediction of genotoxicity in vivo and the understanding of underlying mechanisms. more...

Organism:

Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL18609

156 Samples

Download data: GPR, TXT

(Submitter supplied) Under REACH, the European Community Regulation on chemicals, the testing strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Given that non-genotoxic carcinogens are negative for genotoxicity, this class of carcinogens will not be detected. Therefore, alternative test are urgently needed. Non-genotoxic carcinogens, however, act through different modes of action, which complicates the development of such an assay. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL15125

71 Samples

Download data: CEL, TXT

(Submitter supplied) The current test strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Non-genotoxic carcinogens (NGTXC) are negative for genotoxicity and go undetected. Therefore, alternative tests to detect these chemicals are urgently needed. NGTXC act through different modes of action, which complicates the development of such assays. We have demon­strated recently in primary mouse hepatocytes that some, but certainly not all, NGTXC can be categorized according to their mode of action based on feature detection at a gene expression level (Schaap et al. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17198

88 Samples

Download data: CEL

(Submitter supplied) The current test strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Non-genotoxic carcinogens (NGTXC) are negative for genotoxicity and go undetected. Therefore, alternative tests to detect these chemicals are urgently needed. NGTXC act through different modes of action, which complicates the development of such assays. We have demonstrated recently in primary mouse hepatocytes that some, but certainly not all, NGTXC can be categorized according to their mode of action based on feature detection at a gene expression level (Schaap et al. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL15125

111 Samples

Download data: CEL, TXT

(Submitter supplied) The lack of accurate in vitro assays for predicting in vivo toxicity of chemicals together with new legislations demanding replacement and reduction of animal testing has triggered the development of alternative methods. This study aimed at developing a transcriptomics-based in vitro prediction assay for in vivo genotoxicity. The transcriptomics changes induced in the human liver cell line HepG2 by 34 compounds after treatment for 12h, 24h and 48h were used for the selection of gene-sets that can discriminate between in vivo genotoxins (GTX) and in vivo non-genotoxins (NGTX). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL9101

560 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL9052 GPL13695

16 Samples

Download data: CEL, TXT

(Submitter supplied) Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13695

8 Samples

Download data: CEL, TXT

(Submitter supplied) Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

8 Samples

Download data: TXT

(Submitter supplied) Here, we examined the liver microRNA profile of male Fischer rats exposed through their diet to genotoxic (2-acetylaminofluorene) and epigenetic (phenobarbital, diethylhexylphthalate, methapyrilene HCL, monuron, and chlorendic acid) chemical hepatocarcinogens, as well as to non-hepatocarcinogenic treatments (benzophenone, and diethylthiourea) for three months. The aim of the study was to investigate how liver miRNA profiles relate to mode of action and carcinogenic potential of chemicals.

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by array

Platform:

GPL14889

38 Samples

Download data: TXT

(Submitter supplied) Purpose: Toxicogenomics analyses may provide information about DNA-damaging properties of test compounds but are not routinely used for identification of a genotoxic potential. In this study, metabolically active human HepaRG hepatocarcinoma cells were exposed to six food-relevant genotoxic carcinogens. Method: Transcriptomic responses were analyzed using RNA sequencing technology

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

21 Samples

Download data: TXT