GEO DataSets

(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) 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) RNA-Seq has been increasingly used for the quantification and characterization of transcriptomes. The ongoing development of the technology promises the more accurate measurement of gene expression. However, its benefits over widely accepted microarray technologies have not been adequately assessed, especially in toxicogenomics studies. The goal of this study is to enhance the scientific community's understanding of the advantages and challenges of RNA-Seq in the quantification of gene expression by comparing analysis results from RNA-Seq and microarray data on a toxicogenomics study. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10287

8 Samples

Download data: TXT

(Submitter supplied) MCF-7 and HepG2 cells were exposed to a range of concentrations of benzo(a)pyrene or benzo(e)pyrene (0-5 uM) for up to 48 h and gene expression analysis performed. Keywords: dose response

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

96 Samples

Download data

(Submitter supplied) The number of legacy chemicals without toxicity reference values combined with the rate of new chemical development are overwhelming the capacity of the traditional risk assessment paradigm. More efficient approaches are needed to quantitatively estimate chemical risks. In this study, rats were dosed orally with multiple doses of six chemicals for 5 days, 2, 4, and 13 weeks. Target organs were analyzed for traditional histological and organ weight changes and transcriptional changes using microarrays. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL16985

720 Samples

Download data: CEL

(Submitter supplied) Purpose: The objective of this study is to use Atlantic cod (Gadus morhua) PCLS culture and RNA-seq analysis to map gene expression responses to BaP and EE2 exposure in Atlantic cod. Methods: A total of 8 (3 females and 5 males) juvenile cod (G. morhua) (average body weight 498 g) were used for PCLS (n = 6-8 per group). PCLS preparation and chemical exposure in the culture was performed as previously described (Eide et al., 2014). more...

Organism:

Gadus morhua

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24273

47 Samples

Download data: TXT

(Submitter supplied) Purpose: This study aimed to identify differentially expressed genes and transcripts in zebrafish embryos and larvae following benzo[a]pyrene (BaP) exposure. Methods: Adult zebrafish (2 males × 4 females, N=6 replicate tanks for each treatment) were acclimated for 7 days in an 818 Low Temp Illuminated Incubator (Precision Scientific, Chennai, India) at 28.5°C. Next, adult fish were waterborne exposed to control or 50 μg/L (ppb) BaP for 7 days; ethanol was used as vehicle solvent, and final ethanol concentration was 0.1 mL/L (100 ppm) in all treatment groups. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

10 Samples

Download data: TXT

(Submitter supplied) Human colon carcinoma cells (HCT116) differing in p53 status were exposed to benzo(a)pyrene (BaP) (2.5 and 5 uM for up to 48 h) or anti-benzo(a)pyrene-trans-7,8-dihydrodiol-9,10-epoxide (BPDE)(0.5 and 1 uM for up to 24 h), and their gene expression responses compared by cDNA microarray technology. Keywords: BaP or BPDE exposure

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4348

47 Samples

Download data: GPR

(Submitter supplied) Sickle cell transcriptome was analyzed using whole blood clinical specimens on the Affymetrix Human Exon 1.0 ST arrays and Illumina’s deep sequencing technologies. Data analysis indicated a strong concordance (R=0.64) between exon array and RNA-seq in both gene level and exon level expression of transcripts. The magnitude of fold changes in the expression levels for the differentially expressed genes (p<0.05) was found to be higher in RNA-seq than microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

10 Samples

Download data: CEL

(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:

GPL13916 GPL15933

548 Samples

Download data: CEL

(Submitter supplied) Polycyclic aromatic hydrocarbons (PAHs) are widely distributed, carcinogenic environmental contaminants produced as a consequence of the incomplete combustion of fossil fuels. Benzo[a]pyrene (BaP) is a very extensively studied prototypical PAH. We recently reported a complete lack of change in microRNA (miRNA) expression in adult mouse liver following oral gavage with BaP despite a robust transcriptome response. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL4134 GPL8824

45 Samples

Download data: 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) Twenty-eight days after the initial seeding, the terminally differentiated HepaRG cells were treated with 2 µM benzo[a]pyrene (B[a]P) and benzo[e]pyrene (B[e]P) for 72 hours. Following the treatment, the cells were harvested by mild trypsinization, washed in phosphate-buffered saline, and immediately frozen at −80°C for subsequent analyses. Gene expression profiles in the HepaRG cells treated with B[a]P and B[e]P were investigated using Agilent whole genome 8x60K human microarrays according to the manufacturer’s instructions.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20844

9 Samples

Download data: TXT

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5175 GPL5188

40 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

20 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

20 Samples

Download data: CEL

(Submitter supplied) Purpose: provide evidence that RNA-seq can add information to transcriptome profiling already discovered by other technologies for atopic dermatitis Methods: mRNA profiles of 20 atopic dermatitis were analyzed to compare lesional and non-lesional skin, then transcriptomes found by reads were compared to Microarray and RT-PCR Results:RNA-seq provided complementary genes to AD transcriptome IL-36 and TREM-1 Conclusions: Our study represents the first analysis of lesional AD tissue by RNA-seq and comparison to microarray and RT-PCR

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

40 Samples

Download data: TXT