Expression data from human liver cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Sisir Dutta
PROVIDER: E-GEOD-6878 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
PCB congener specific oxidative stress response by microarray analysis using human liver cell line.
De Supriyo S Ghosh Somiranjan S Chatterjee Raghunath R Chen Y-Q YQ Moses Linda L Kesari Akanchha A Hoffman Eric P EP Dutta Sisir K SK
Environment international 20100717 8
In this study we have examined the effect of exposure to different congeners of PCBs and their role in oxidative stress response. A metabolically competent human liver cell line (HepG2) was exposed with two prototype congeners of PCBs: coplanar PCB-77 and non-coplanar PCB-153. After the predetermined times of exposure (0-24h) at 70 μM concentration, the HepG2 cells showed significant apoptotic changes by fluorescent microscopy after 12h of exposure. Gene set enrichment analysis (GSEA) identified ...[more]
Similar Datasets
Project description:Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases is not fully understood. The knowledge of global gene expression will help us to devlop early diagnostic biomarkers for PCB induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of PCB153 on human liver cells leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. Keywords: time course The HepG2 cells were grown for 48 hours in DMEM supplemented with 10% FBS and 1X Pennicillin-Streptromycin and treated with PCB153 for different times. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
2010-07-21 | E-GEOD-6494 | biostudies-arrayexpress
Project description:Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of different diseases is not fully understood. The knowledge of global gene expression will help us to develop early diagnostic biomarkers for PCB induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of PCB77 on human liver cells leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. Keywords: time course The HepG2 cells were grown for 48 hours in DMEM supplemented with 10% FBS and 1X Pennicillin-Streptromycin and treated with PCB77 for different times. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
2010-07-22 | E-GEOD-6869 | biostudies-arrayexpress
Project description:Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases is not fully understood. The knowledge of global gene expression will help us to devlop early diagnostic biomarkers for PCB induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of PCB77 on human Kidney cells leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. Keywords: time course The HK2 cells are grown in Keratinocyte-Serum Free Medium supplemented 5ng/ml recombinant epidermal growth factor and 0.05mg/ml bovinepituitary extract and 1X Pennicilllin-Streptromycin and were treated with 40 micro molar of PCB77 with different exposure time. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
2012-08-02 | E-GEOD-23493 | biostudies-arrayexpress
Project description:Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for PCB induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of PCB 138 exposure to human PBMC leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. Keywords: PCB 138 Exposures PBMC cells are grown for 48 hours in RPMI 1640 supplemented with 10% FBS and 1X Pennicilllin-Streptromycin with 1.25 mircogram/ml PHA-M and 0.15% (v/v)pokeweed mitogen and 50 microgram Beta-mercaptoethanol.Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
2011-04-19 | E-GEOD-22632 | biostudies-arrayexpress
Project description:Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for PCB induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of PCB 153 exposure to human PBMC leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. PBMC cells are grown for 48 hours in RPMI 1640 supplemented with 10% FBS and 1X Pennicilllin-Streptromycin with 1.25 mircogram/ml PHA-M and 0.15% (v/v)pokeweed mitogen and 50 microgram Beta-mercaptoethanol.Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
2011-04-19 | E-GEOD-22667 | biostudies-arrayexpress
Project description:Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of different diseases and disorders are not fully understood. The knowledge of global gene expression will help us to develop early disease or disorder biomarkers for PCB induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of mixed PCB exposure at Slovak Human equivalance Level on human PBMC leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. PBMC cells are grown for 48 hours in RPMI 1640 supplemented with 10% FBS and 1X Pennicilllin-Streptromycin with 1.25 microgram/ml PHA-M and 0.15% (v/v)pokeweed mitogen and 50 microgram beta-mercaptoethanol. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
2015-06-22 | E-GEOD-22668 | biostudies-arrayexpress
Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the mesenchymal and epithelial compartments of the e13 mouse bladder. Keywords: Mouse embryonic day 13 bladder mesenchyme and epithelium. FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were microdissected, cut just above the ureters, and treated with 20 µM EDTA for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix MOE430 microarray chip
2009-01-16 | E-GEOD-12618 | biostudies-arrayexpress
Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of micro dissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the mesenchymal and epithelial compartments of the E13 mouse bladder neck/urethral compartment. FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were microdissected and cut just below the ureters. Since the EDTA dissociation was ineffective, the bladder neck and urethra were collected and treated with 1 mg/ml trypsin in Tyrode's solution for 20 minutes at 37°C. The layers were separated using a fine needle and rimming. The samples were placed in RLT and stored at -80°C. RNA was prepared and the Epicentre 2-round amplification scheme described under the Lessard Group Protocols on the GUDMAP pages were performed. The amplified RNA was examined with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
2009-04-24 | E-GEOD-15794 | biostudies-arrayexpress
Project description:The mammalian FoxO transcription factors - FoxO1, FoxO3, FoxO4 - function in the nucleus to direct transcription of specific gene targets governing cellular survival, proliferation, metabolism, differentiation and oxidative defense. Activation of PI3K by extracellular growth factors leads to AKT-mediated phosphorylation of FoxO1, FoxO3 and FoxO4, resulting in their sequestration in the cytoplasm such that they are unable to regulate their gene targets. Our study identified FoxOs as novel tumor suppressors in kidney cancer (Gan et al, 2010, Cancer Cell). To understand the tumor suppression function of FoxOs in kidney cancer cells, we performed gene expression profiling in human kidney cancer cells upon FoxO1 or FoxO3 reactivation in order to identify the key transcriptomic alterations mediating FoxO tumor suppression function in kidney cancer cells. We generated RCC4 and UMRC2 cell lines (two human kidney cancer cells with low endogenous FoxO1 and FoxO3 expression) with stable expression of FoxO1(TA)ERT2 or FoxO3(TA)ERT2 construct, which expressed a fusion protein consisting of FoxO(TA) (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety. We documented that the FoxO(TA)ERT2 fusion protein sequestered FoxO(TA) in the cytoplasm and that 4OHT treatment resulted in rapid translocation of FoxO(TA)ERT2 into the nucleus. We also established stable cell lines with ERT2 expression as control cell lines. (For simplicity, ERT2, FoxO1(TA)ERT2 and FoxO3(TA)ERT2 cell lines will be referred to as EV (empty vector), FoxO1 and FoxO3, respectively, hereafter). We then conducted comparative transcriptome analysis (using the Human Genome U133 Plus 2.0 Array) of EV, FoxO1, or FoxO3-expressing RCC4 and UMRC2 cells at 12 hours with or without 100 nm 4OHT treatment (cultured in DMEM+10% FBS with puromycin selection). To enrich for more proximal actions of FoxO, we selected the 12 hour time point as time course studies revealed dramatic transcriptional changes of known FoxO targets (such as Cyclin D1), yet no discernable cellular phenotypes (apoptosis and cell cycle arrest). We generated 4 transcriptome datasets: FoxO1 RCC4, FoxO3 RCC4, FoxO1 UMRC2, and FoxO3 UMRC2 (by comparing transcriptome data with or without 4OHT treatment), and normalized these transcriptome data against 4OHT-treated EV cells, which show modest 4OHT-induced transcriptional changes.
2011-10-20 | E-GEOD-23926 | biostudies-arrayexpress
Project description:A triclosan-ciprofloxacin cross-resistant mutant strain of Staphylococcus aureus displays an alteration in the expression of several cell membrane structural and functional genes. Triclosan is an antimicrobial agent found in many consumer products. Several studies have demonstrated that triclosan inhibits the bacterial fatty acid biosynthetic enzyme, enoyl-ACP reductase (FabI). Studies have also demonstrated that decreased susceptibility to triclosan correlates with ciprofloxacin resistance in several bacteria. In these bacteria, resistance to both drugs maps to genes encoding multi-drug efflux pumps. The focus of this study was to determine whether triclosan resistance contributes to ciprofloxacin resistance in Staphylococcus aureus. Gene expression profiling was performed to compare the gene expression profiles of unexposed and triclosan-exposed wild-type and JJ5 determined that an alteration in global gene expression possibly resulting in a change in cell membrane structure and function is likely responsible for triclosan and ciprofloxacin resistance in JJ5. Keywords: Treatment response WT and triclosan resistant mutant were treated with triclosan and their gene expression was compared to their untreated conterparts.
2010-05-26 | E-GEOD-5799 | biostudies-arrayexpress