Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA153319 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study evaluated human embryonic stem cells (hESC) and their differentiated fibroblastic progenies as cellular models for genotoxicity screening. The DNA damage response of hESCs and their differentiated fibroblastic progenies were compared to a fibroblastic cell line (HEPM, CRL1486) and primary cultures of peripheralblood lymphocytes (PBL), upon exposure to gamma irradiation.
2014-07-30 | GSE36355 | GEO
Project description:Validation study of a focused microarray for evaluation of undifferentiated rat ESCs.Using a focused microarray, undifferentiated embryonic stem cells (ESCs) can be distinguished from differentiated ESCs and other cells derived from the early embryo since they have a unique gene expression pattern associated with pluripotency and lack of markers of differentiation. To date, however, such an array has not been developed for the rat species and differences in genomes of rat and human or rat and mouse preclude the use of ESC focused human or mouse microarrays for the rat. Here, we developed a focused microarray for screening rat ESCs and provide validation data that this array can distinguish undifferentiated rat ESCs from rat trophoblast stem cells (TS), rat extraembryonic endoderm cells (XEN), mouse embryonic fibroblast feeder cells (MEFs) and rat ESCs that have been differentiated in vitro. We used this tool to compare rat ESCs which have been expanded in a conventional rat ESC medium containing two inhibitors, e.g., GSK3 and MEK inhibitors, and leukemia inhibitory factor (LIF), and found expression of Cdx2, a gene associated with trophoblast determination. The rat ESC focused microarray described in this report has utility for rapid screening rat ESCs. This will enable optimization of culture conditions in the future. qRT-PCR gene expression profiling of undifferentiated ESCs and iPS cells. Equal amounts (1000ng) total RNA from each cell line was used in independent trials conducted by two investigators, these are technical replicates.
2014-09-25 | E-GEOD-61731 | biostudies-arrayexpress
Project description: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). By combining publicly available results for these chemicals from standard in vitro genotoxicity studies with transcriptomics, we developed several prediction models. These models were validated by means of an additional set of 28 chemicals. The study investigated differential gene expression in HepG2 cell line mRNA following 12 hours of exposure to 34 different compounds and their solvents; 24 and 48 hours of exposure to 62 different compounds and their solvents. Three biological replicates per compound/solvent. In total 560 arrays .
2012-08-02 | E-GEOD-28878 | biostudies-arrayexpress
Project description: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). By combining publicly available results for these chemicals from standard in vitro genotoxicity studies with transcriptomics, we developed several prediction models. These models were validated by means of an additional set of 28 chemicals.
2012-08-02 | GSE28878 | GEO
Project description:Cellular models of hepatogenesis using embryonic stem cells
| PRJNA391823 | ENA
Project description:Validation study of a focused microarray for evaluation of undifferentiated rat ESCs.Using a focused microarray, undifferentiated embryonic stem cells (ESCs) can be distinguished from differentiated ESCs and other cells derived from the early embryo since they have a unique gene expression pattern associated with pluripotency and lack of markers of differentiation. To date, however, such an array has not been developed for the rat species and differences in genomes of rat and human or rat and mouse preclude the use of ESC focused human or mouse microarrays for the rat. Here, we developed a focused microarray for screening rat ESCs and provide validation data that this array can distinguish undifferentiated rat ESCs from rat trophoblast stem cells (TS), rat extraembryonic endoderm cells (XEN), mouse embryonic fibroblast feeder cells (MEFs) and rat ESCs that have been differentiated in vitro. We used this tool to compare rat ESCs which have been expanded in a conventional rat ESC medium containing two inhibitors, e.g., GSK3 and MEK inhibitors, and leukemia inhibitory factor (LIF), and found expression of Cdx2, a gene associated with trophoblast determination. The rat ESC focused microarray described in this report has utility for rapid screening rat ESCs. This will enable optimization of culture conditions in the future.
2012-09-10 | GSE30582 | GEO
Project description:Validation study of a focused microarray for evaluation of undifferentiated rat ESCs.Using a focused microarray, undifferentiated embryonic stem cells (ESCs) can be distinguished from differentiated ESCs and other cells derived from the early embryo since they have a unique gene expression pattern associated with pluripotency and lack of markers of differentiation. To date, however, such an array has not been developed for the rat species and differences in genomes of rat and human or rat and mouse preclude the use of ESC focused human or mouse microarrays for the rat. Here, we developed a focused microarray for screening rat ESCs and provide validation data that this array can distinguish undifferentiated rat ESCs from rat trophoblast stem cells (TS), rat extraembryonic endoderm cells (XEN), mouse embryonic fibroblast feeder cells (MEFs) and rat ESCs that have been differentiated in vitro. We used this tool to compare rat ESCs which have been expanded in a conventional rat ESC medium containing two inhibitors, e.g., GSK3 and MEK inhibitors, and leukemia inhibitory factor (LIF), and found expression of Cdx2, a gene associated with trophoblast determination. The rat ESC focused microarray described in this report has utility for rapid screening rat ESCs. This will enable optimization of culture conditions in the future.
2014-09-25 | GSE61731 | GEO
Project description:The conventional battery for genotoxicity testing is not well suited to assessing the large number of chemicals needing evaluation. Traditional in vitro tests lack throughput, provide little mechanistic information, and have poor specificity in predicting in vivo genotoxicity. New Approach Methodologies (NAMs) aim to accelerate the pace of hazard assessment and reduce reliance on in vivo tests that are time-consuming and resource-intensive. As such, high-throughput transcriptomic and flow cytometry-based assays have been developed for modernized in vitro genotoxicity assessment. This includes: the TGx-DDI transcriptomic biomarker (i.e., 64-gene expression signature to identify DNA damage-inducing (DDI) substances), the MicroFlow® assay (i.e., a flow cytometry-based micronucleus (MN) test), and the MultiFlow® assay (i.e., a multiplexed flow cytometry-based reporter assay that yields mode-of-action (MoA) information). The objective of this study was to investigate the utility of the TGx-DDI transcriptomic biomarker, multiplexed with the MicroFlow® and MultiFlow® assays, as an integrated NAM-based testing strategy for screening data-poor compounds prioritized by Health Canada’s New Substances Assessment and Control Bureau. Human lymphoblastoid TK6 cells were exposed to 3 control and 10 data-poor substances, using a 6-point concentration range. Gene expression profiling was conducted using the targeted TempO-SeqTM assay, and the TGx-DDI classifier was applied to the dataset. Classifications were compared with those based on the MicroFlow® and MultiFlow® assays. Benchmark Concentration (BMC) modeling was used for potency ranking. The results of the integrated hazard calls indicate that five of the data-poor compounds were genotoxic in vitro, causing DNA damage via a clastogenic MoA, and one via a pan-genotoxic MoA. Two compounds were likely irrelevant positives in the MN test; two are considered possibly genotoxic causing DNA damage via an ambiguous MoA. BMC modeling revealed nearly identical potency rankings for each assay. This ranking was maintained when all endpoint BMCs were converted into a single score using the Toxicological Prioritization (ToxPi) approach. Overall, this study contributes to the establishment of a modernized approach for effective genotoxicity assessment and chemical prioritization for further regulatory scrutiny. We conclude that the integration of TGx-DDI, MicroFlow®, and MultiFlow® endpoints is an effective NAM-based strategy for genotoxicity assessment of data-poor compounds.
2022-11-15 | GSE213454 | GEO
Project description:Pooled genetic screening with CRISPR/Cas9 has enabled genome-wide high-resolution assignment of genes to phenotypes. To assess the effect of a given genetic perturbation, each sgRNA must be evaluated in hundreds of cells to overcome stochastic genetic drift and obtain robust results. In complex models that display particularly high heterogeneity, such as organoids or tumors transplanted into mice however, sufficient representation typically requires unreasonable scaling, thus preventing genome-wide screens at high resolution. Here we present CRISPR-StAR, a screening paradigm that overcomes intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by leveraging internal controls generated through activating sgRNAs only in half of the progenies of each cell. We use CRISPR-StAR to reveal in vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking to a conventional screening setup highlights the improved data quality this technology delivers. We anticipate CRISPR-StAR to set a new standard for genetic screening in complex models, foremost in vivo.
2024-11-05 | GSE262307 | GEO
Project description:Pooled genetic screening with CRISPR/Cas9 has enabled genome-wide high-resolution assignment of genes to phenotypes. To assess the effect of a given genetic perturbation, each sgRNA must be evaluated in hundreds of cells to overcome stochastic genetic drift and obtain robust results. In complex models that display particularly high heterogeneity, such as organoids or tumors transplanted into mice however, sufficient representation typically requires unreasonable scaling, thus preventing genome-wide screens at high resolution. Here we present CRISPR-StAR, a screening paradigm that overcomes intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by leveraging internal controls generated through activating sgRNAs only in half of the progenies of each cell. We use CRISPR-StAR to reveal in vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking to a conventional screening setup highlights the improved data quality this technology delivers. We anticipate CRISPR-StAR to set a new standard for genetic screening in complex models, foremost in vivo.
2024-11-05 | GSE262308 | GEO