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High-Throughput Transcriptomics Platform for Screening Environmental Chemicals
We screened 44 chemicals in MCF7 cells in concentration response and generated HTTr data using the TempO-Seq hWTv1 assay. First, we provide an outline of the quality of the HTTr data based on a set of QC metrics we developed for this platform. Second, we evaluate the reproducibility and mechanistic accuracy of the HTTr platform using inter-plate analysis of reference samples and comparison of reference chemical treatment effects with CMAP signatures, respectively. Third, we summarize the concentration-dependent HTTr responses for all 44 chemicals to stratify them in terms of their overall effect on the transcriptome. Fourth, we present a new gene signature based concentration-response analysis that provides potency estimates for perturbation of cellular biology (ie, BPACs).
This dataset is associated with the following publication:
Harrill, J., L. Everett, D. Haggard, T. Sheffield, J. Bundy, C. Willis, R. Thomas, I. Shah, and R. Judson. High-Throughput Transcriptomics Platform for Screening Environmental Chemicals. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 181(1): 68-89, (2021).
Resources
1 resource available
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https://gaftp.epa.gov/COMPTOX/CCTE_Publication_Data/BCTD_Publication_Data/Everett/HTTr_Pilot_FigShare/
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "020:00" ] |
| contactPoint |
{ "fn": "Joshua Harrill", "hasEmail": "mailto:harrill.joshua@epa.gov" } |
| description | We screened 44 chemicals in MCF7 cells in concentration response and generated HTTr data using the TempO-Seq hWTv1 assay. First, we provide an outline of the quality of the HTTr data based on a set of QC metrics we developed for this platform. Second, we evaluate the reproducibility and mechanistic accuracy of the HTTr platform using inter-plate analysis of reference samples and comparison of reference chemical treatment effects with CMAP signatures, respectively. Third, we summarize the concentration-dependent HTTr responses for all 44 chemicals to stratify them in terms of their overall effect on the transcriptome. Fourth, we present a new gene signature based concentration-response analysis that provides potency estimates for perturbation of cellular biology (ie, BPACs). This dataset is associated with the following publication: Harrill, J., L. Everett, D. Haggard, T. Sheffield, J. Bundy, C. Willis, R. Thomas, I. Shah, and R. Judson. High-Throughput Transcriptomics Platform for Screening Environmental Chemicals. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 181(1): 68-89, (2021). |
| distribution |
[ { "title": "https://gaftp.epa.gov/COMPTOX/CCTE_Publication_Data/BCTD_Publication_Data/Everett/HTTr_Pilot_FigShare/", "accessURL": "https://gaftp.epa.gov/COMPTOX/CCTE_Publication_Data/BCTD_Publication_Data/Everett/HTTr_Pilot_FigShare/" } ] |
| identifier | https://doi.org/10.23719/1522614 |
| keyword |
[ "TempO-Seq", "computational toxicology", "high-throughput screening", "transcriptomics" ] |
| license | https://pasteur.epa.gov/license/sciencehub-license.html |
| modified | 2020-12-22 |
| programCode |
[ "020:000" ] |
| publisher |
{ "name": "U.S. EPA Office of Research and Development (ORD)", "subOrganizationOf": { "name": "U.S. Environmental Protection Agency", "subOrganizationOf": { "name": "U.S. Government" } } } |
| references |
[ "https://doi.org/10.1093/toxsci/kfab009" ] |
| rights |
null
|
| title | High-Throughput Transcriptomics Platform for Screening Environmental Chemicals |
