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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).
Complete Metadata
| 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 |
