Human toxicology-relevant cell lines treated with three doses of 34 chemical compounds
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Jay Tiesman
PROVIDER: E-GEOD-69851 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This study provides an evaluation of changes in gene expression associated with treating human HEPG2 cells with 34 different chemical compounds. Gene expression experiments studies were performed in triplicate (n=3) with the cells for each replicate treated and harvested on separate days. This series is part of a SuperSeries in which human toxicology-relevant cell lines were treated with three doses of 34 chemical compounds (and corresponding vehicle controls) for 6 hours. Each compound/vehicle treatment group was an individual study performed at different times. Each study was analyzed separately and themes common between studies were reported.
2016-03-28 | E-GEOD-69850 | biostudies-arrayexpress
Project description:This study provides an evaluation of changes in gene expression associated with treating human HepaRG cells with 34 different chemical compounds. Gene expression experiments studies were performed in triplicate (n=3) with the cells for each replicate treated and harvested on separate days. This series is part of a SuperSeries in which human toxicology-relevant cell lines were treated with three doses of 34 chemical compounds (and corresponding vehicle controls) for 6 hours. Each compound/vehicle treatment group was an individual study performed at different times. Each study was analyzed separately and themes common between studies were reported.
2016-03-28 | E-GEOD-69844 | biostudies-arrayexpress
Project description:This study provides an evaluation of changes in gene expression associated with treating human MCF7 cells with 34 different chemical compounds. Gene expression experiments studies were performed in triplicate (n=3) with the cells for each replicate treated and harvested on separate days. This series is part of a SuperSeries in which human toxicology-relevant cell lines were treated with three doses of 34 chemical compounds (and corresponding vehicle controls) for 6 hours. Each compound/vehicle treatment group was an individual study performed at different times. Each study was analyzed separately and themes common between studies were reported.
2016-03-28 | E-GEOD-69845 | biostudies-arrayexpress
Project description:This study provides an evaluation of changes in gene expression associated with treating human Ishikawa cells with 34 different chemical compounds. Gene expression experiments studies were performed in triplicate (n=3) with the cells for each replicate treated and harvested on separate days. This series is part of a SuperSeries in which human toxicology-relevant cell lines were treated with three doses of 34 chemical compounds (and corresponding vehicle controls) for 6 hours. Each compound/vehicle treatment group was an individual study performed at different times. Each study was analyzed separately and themes common between studies were reported.
2016-03-28 | E-GEOD-69849 | biostudies-arrayexpress
Project description:For the purpose of mechanism-based risk assessment, we investigated temporal concentration-dependent responses in cultures of PHH and HepaRG cells exposed to three cosmetics ingredients, 2,7-naphthalenediol (NPT), triclosan (TCS) and butylated hydroxytoluene (BHT), that are suspected to have liver injury liability. To facilitate the identification of early KEs and visualisation of their development over time, samples were collected at 4 time points, namely 8 and 24 hours (single exposure), 48 and 72 hours (daily repeated exposure), after exposure to a broad concentration range. Concentrations were selected based on the estimated Cmax of the cosmetic ingredients. The selected maximum concentration was set at approximately 100x Cmax, whilst the minimum tested concentration was approximately 0.2x Cmax. The large concentration range allowed to apply benchmark concentration (BMC) modelling on individual genes as well as gene co-expression networks to derive in vitro transcriptomics benchmark concentrations (BMCs) and assess their suitability to be used as PoD in chemical risk assessment.
2024-03-01 | E-MTAB-12677 | biostudies-arrayexpress
Project description:For the purpose of mechanism-based risk assessment, we investigated temporal concentration-dependent responses in cultures of PHH and HepaRG cells exposed to three drugs, acetaminophen (APAP), cyclosporine A (CSA) and valproic acid (VPA), that have a high liability for drug-induced liver injury. To facilitate the identification of early KEs and visualisation of their development over time, samples were collected at 4 time points, namely 8 and 24 hours (single exposure), 48 and 72 hours (daily repeated exposure), after exposure to a broad concentration range. Concentrations were selected based on the reported total Cmax of each drug. As these are approved drugs currently on the market, they are not expected to induce overt adverse effects around Cmax. Therefore, the selected maximum concentration was set at approximately 30x Cmax, whilst the minimum tested concentration was approximately 0.1x Cmax. The large concentration range allowed to apply benchmark concentration (BMC) modelling on individual genes as well as gene co-expression networks to derive in vitro transcriptomics benchmark concentrations (BMCs) and assess their suitability to be used as PoD in chemical risk assessment.
2024-03-01 | E-MTAB-12668 | biostudies-arrayexpress
Project description:In this study we conducted transcriptomics analyses of: (i) liver samples from patients suffering from acetaminophen-induced acute liver failure (n=3) and from healthy livers (n=2) and (ii) hepatic cell systems exposed to acetaminophen, including their respective vehicle controls. The investigated in vitro systems are: HepaRG cells, HepG2 cells and a novel human skinpostnatal stem cell-derived model i.e. human skin-precursors-derived hepatocyte-like cells (hSKP-HPC). Clinical samples were obtained after surgical removal of the explant liver of patients diagnosed with ALF due to acetaminophen intoxication and treated by orthotopic liver transplantation (n=3). Samples from healthy livers were obtained from individuals deceased from brain damage (n=2). Different samples of hSKP, HepG2 and HepaRG were obtained from the same cell batch of each cell system. All cells were exposed for 24 hours to their corresponding sub cytotoxic concentrations (IC10): IC10(hSKP-HPC)=18mM; IC10(HepaRG)=13mM; IC10(HepG2)=2mM. Experiments were conducted in triplicate. This dataset is part of the TransQST collection.
2015-11-04 | E-GEOD-74000 | biostudies-arrayexpress
Project description:Approximately 2x106 CL1-5 and H23 cells were seeded on 10-cm dishes with RPMI-1640 medium containing 10% fetal bovine serum. After the cells covered 80% of the dish, cells were serum-starved for 24 h in RPMI-1640 medium. CL1-5 and H23 cell lysates were harvested, trypsinized and analyzed by using LTQ-Orbitrap XL and LTQ-Orbitrap Discovery, respectively. Halobacterium salinarum NRC-1 (ATCC700922) starter culture was prepared by inoculating a single colony in 5 mL of Halobacterium medium containing trace metals (CM+) and grown at 37 °C with shaking at 225 rpm for one week. An aliquot of 300 μL of the culture was spread on 15-cm diameter CM+ plates containing 2% of agarose. After 7~10 days of incubation at 37 °C, the GVs from cells on 10 plates were harvested using the centrifugation facilitated flotation method as previously described except the GVs were washed for a total of 5 times instead of the suggested 3 times to remove nonspecific bound proteins.(29) After collecting the gas vesicles in the primary cell lysate, the cell membrane and residual GV were removed by ultracentrifugation at 53 000× g, 4 °C for 16 h twice to obtain the GV-depleted lysate (GVD). GVD lysate was harvested, trypsinized and analyzed by using LC-MS/MS ( LTQ-Orbitrap XL). The H. salinarum strain NRC-1 was grown in complex medium (CM+) at 37 oC with shaking (200 rpm) to an OD600 of 0.5 (early exponential phase. The cultures were then subjected to an additional hour of incubation at 37 oC for preparation of proteins. The total lysate was harvested, trypsinized and analyzed by using LC-MS/MS (LTQ-Orbitrap Discovery). All MS raw data in Thermo XCalibur (version 2.0.7) binary format were converted to the mzXML open data format using a modified version of the ReAdW program. SEQUEST (version 27) was applied to search the MS/MS spectra against the forward and reverse (decoy) protein sequences of H. salinarum (2,427 proteins; EMBL-EBI Integr8, www.ebi.ac.uk/integr8/EBI-Integr8-HomePage.do) or human (38,425 proteins) plus bovine (22,863 proteins) (GenBank reference sequences, www.ncbi.nlm.nih.gov). SEQUEST results were further processed using the Trans Proteomic Pipeline.
2020-01-14 | PXD000082 | Pride
Project description:Pulmonary fibrosis is a chronic, progressive, and lethal interstitial lung disease. It is characterized by extracellular matrix deposition, fibroblast proliferation, and accumulation. Fibroblasts from normal or UIP histology were cultured and analyzed. Keywords: Fibroblasts from normal histology lung tissue or UIP histology lung tissue Five samples of primary human lung fibroblasts were obtained from explanted lungs of patients with Usual Interstitial Pneumonia (UIP) at the University of Pittsburgh Medical Center (Pittsburgh, PA, USA) and three samples of primary normal human lung fibroblasts were acquired from normal histololgy lung tissues of organ donors. The experimental protocol was approved by the University of Pittsburgh Institutional Reviews Board (IRB). Total RNA was extracted and used as a template to generate double-stranded cDNA and biotin-labeled cRNA, as recommended by the manufacturer of the arrays. Fragmented cRNA was hybridized to Codelink Uniset I slides. After hybridization, arrays were washed and stained with streptavidin-AlexaFluor 647. The arrays were scanned using a Genepix 4000B microarray scanner. Images were analyzed using Codelink expression II analysis suite, and visually inspected for defects and quality control parameters as recommended by the manufacturer.
2010-06-21 | E-GEOD-10921 | biostudies-arrayexpress
Project description:Current approaches to the preclinical investigation for novel cancer therapies rely heavily on the use of traditional cancer cell lines maintained in serum-containing conditions. The discrepancy between promising preclinical efficacy and clinical outcome of most novel anticancer agents emphasizes a need for developing predictive preclinical models that preserve the integrity of original patient tumors, including cancer stem cell (CSC) compartment. In this study, we isolate and characterize CSCs from a non-small cell lung cancer cell line, NCI-H1299, by selectively propagating the cells in a stem-cell culture condition. Isolated CSCs proliferated as nonadherent spheroids, displayed capacity to differentiate and self-renew and exhibited higher tumorigenic potential compared to the parental cells. The gene expression profiles of NCI-H1299 parental cells (serum-containing medium), CSCs (stem-cell medium), and xenograft tumor derived from both cell types were studied by Affymetrix array analysis
2010-07-30 | E-GEOD-21612 | biostudies-arrayexpress