High-throughput transcriptomics platform for screening hepatotoxicants
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA638385 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11966700.fastq.gz | Fastqsanger.gz | |||
| SRR11966800.fastq.gz | Fastqsanger.gz | |||
| SRR11966900.fastq.gz | Fastqsanger.gz | |||
| SRR11966701.fastq.gz | Fastqsanger.gz | |||
| SRR11966801.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 372 |
Similar Datasets
Project description:We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants.
2021-09-01 | GSE152128 | GEO
Project description:High-Throughput Transcriptomics Platform for Screening Environmental Chemicals
| PRJNA683595 | ENA
Project description:New approach methodologies (NAMs) that efficiently provide information about chemical hazard without using whole animals are needed to accelerate the pace of chemical safety assessments. Technological advancements in gene expression assays have made in vitro high-throughput transcriptomics (HTTr) a feasible option for NAMs-based hazard characterization of environmental chemicals. In the present study, we evaluated the Templated Oligo with Sequencing Readout (TempO-Seq) assay for HTTr concentration-response screening of a small set of chemicals in the human-derived MCF7 cell model. Our experimental design included a variety of reference samples and reference chemical treatments in order to objectively evaluate TempO-Seq assay performance. To facilitate analysis of these data, we developed a robust and scalable bioinformatics pipeline using open-source tools. We also developed a novel gene expression signature-based concentration-response modeling approach and compared the results to a previously implemented workflow for concentration-response analysis of transcriptomics data using BMDExpress. Analysis of reference samples and reference chemical treatments demonstrated highly reproducible differential gene expression signatures. In addition, we found that aggregating signals from individual genes into gene signatures prior to concentration-response modeling yielded in vitro transcriptional biological pathway altering concentrations (BPACs) that were closely aligned with previous ToxCast high-throughput screening (HTS) assays. Often these identified signatures were associated with the known molecular target of the chemicals in our test set as the most sensitive components of the overall transcriptional response. This work has resulted in a novel and scalable in vitro HTTr workflow that is suitable for high throughput hazard evaluation of environmental chemicals.
2021-01-25 | GSE162855 | GEO
Project description:New approach methodologies (NAMs) that efficiently provide information about chemical hazard without using whole animals are needed to accelerate the pace of chemical risk assessments. Technological advancements in gene expression assays have made in vitro high-throughput transcriptomics (HTTr) a feasible option for NAMs-based hazard characterization of environmental chemicals. In this study, we evaluated the Templated Oligo with Sequencing Readout (TempO-Seq) assay for HTTr concentration-response screening of a small set of chemicals in the human-derived MCF7 cell model. Our experimental design included a variety of reference samples and reference chemical treatments in order to objectively evaluate TempO-Seq assay performance. To facilitate analysis of these data, we developed a robust and scalable bioinformatics pipeline using open-source tools. We also developed a novel gene expression signature-based concentration-response modeling approach and compared the results to a previously implemented workflow for concentration-response analysis of transcriptomics data using BMDExpress. Analysis of reference samples and reference chemical treatments demonstrated highly reproducible differential gene expression signatures. In addition, we found that aggregating signals from individual genes into gene signatures prior to concentration-response modeling yielded in vitro transcriptional biological pathway altering concentrations (BPACs) that were closely aligned with previous ToxCast high-throughput screening assays. Often these identified signatures were associated with the known molecular target of the chemicals in our test set as the most sensitive components of the overall transcriptional response. This work has resulted in a novel and scalable in vitro HTTr workflow that is suitable for high-throughput hazard evaluation of environmental chemicals.
| S-EPMC10194851 | biostudies-literature
Project description:Chromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less characterized in the non-coding genome, partially due to the lack of a platform to readily evaluate boundary-associated activities of putative DNA sequences. Here we report SHIELD (Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains), a novel platform tailored for the high-throughput screening of barrier-type DNA elements in human cells. SHIELD takes advantage of the high specificity of serine integrase at heterochromatin, and exploits the natural heterochromatin spreading inside LADs for the discovery of potent barrier elements. We adopted SHIELD to evaluate the barrier activity of 1000 DNA elements in a high-throughput manner and identified 8 novel elements with barrier activities comparable to the core region of cHS4 element. SHIELD should greatly facilitate the discovery of novel barrier DNA elements from the non-coding genome in human cells.
2023-08-01 | GSE236198 | GEO
Project description:Major advances have been made to develop an automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. An in-solution digest strategy is employed to generate peptides from the extracted proteins for LC-MS analysis in the 384-well plate. Method evaluation utilized HeLa cells cultured in the 384-well plate ranging from 500 – 10,000 cells. Digestion efficiency was excellent in comparison to the commercial digest peptides standard with minimal sample loss while improving sample preparation throughput by 20 – 40 fold. Analysis of six human cell types, which included two primary cell samples identified and quantified approximately 4,000 proteins for each sample in a single LC-MS/MS injection with as little as 100 – 10,000 cells depending on cell type demonstrating universality of the platform. Implementation of the comprehensive 384-well format protocol for processing cells to clean digested peptides enables large-scale biomarker validation and compound screening through proteomic analysis.
2021-06-14 | PXD019733 | Pride
Project description:SHIELD: A platform for high-throughput screening of barrier DNA elements in human cells
| PRJNA989234 | ENA
Project description:High-throughput high-multiplexed screening for splicing factors
| PRJNA854891 | ENA
Project description:Major advances have been made to improve the sensitivity of mass analyzers, spectral quality, and the speed of data processing enabling more comprehensive proteome discovery and quantitation. While focus has recently begun shifting toward robust proteomic sample preparation efforts, a high throughput proteomics sample preparation is still lacking. We report the development of a highly-automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. Digestion efficiency was excellent in comparison to a commercial digest peptide standard with minimal sample loss while improving sample preparation throughput by 20- to 40-fold (<1 min/sample for entire process from cells to clean peptides). Analysis of six human cell types, which included two primary cell samples, identified and quantified approximately 4,000 proteins for each sample in a single HPLC-MS/MS injection with only 100 -10,000 cells, thus demonstrating universality of the platform.
2021-06-14 | PXD023374 | Pride
Project description:Myeloid-derived suppressor cells are a heterogeneous cell population of incompletely differentiated immune cells. They are known for suppressing T cell activity and are implicated in multiple chronical diseases, which makes them an attractive drug target for the pharmaceutical industry. Here, we differentiated mouse MDSC from a progenitor cell line and used quantitative (phospho)proteomics to quantify more than 7,000 proteins and phosphorylation sites that enable the characterization of MDSC on a molecular level. Based on this differentiation protocol, we investigated the effects of the well-studied MDSC drugs Entinostat and Mocetinostat on a proteomewide level and established a high-throughput drug screening platform. We assessed the effects on T cell proliferation and INF-γ secretion of ~21,000 small molecules in a MDSC/T cell coculture setup. The most promising candidates were further validated in a screening setup using human MDSC. Finally, a proteomics experiment showed the significant upregulation of several proteins associated with the reduction of reactive oxygen species, suggesting the potential mode of action of this compound.
2023-08-15 | PXD043407 | Pride