DOI: 10.5281/zenodo.18292966
title: Longitudinal responses of human cancer cell lines to oncology drugs

description: Data Description

Title: Longitudinal responses of human cancer cell lines to oncology drugs  Date: 2026-01-18Authors: Darren R. Tyson, Joshua A. Bauer, Sarah M. Groves, Vito Quaranta, Alexander LubbockAffiliation: Vanderbilt University (at time of data generation)Contact: darren at cancersysbio.org

Context

This dataset contains cell count data derived from fluorescence microscopy of various human cancer cell lines expressing nuclear-localized fluorescent proteins (general approach is described in Harris et al., 2016 and Meyer et al., 2021; see citations below). These data were originally hosted on the Thunor web application hosted by Vanderbilt University that has since gone offline.

File Structure

The dataset consists of 3 CSV files:



HTS001.csv: PC-9 and derivatives (DS3, DS7, DS8, DS9, PC9-MGH, PC9-BR1) seeded at 200 cells per well, treated with EGFR-centric panel of inhibitors in 4-fold dilutions, and imaged for 5 days   

HTS003.csv: PC-9 and derivatives seeded at 300 cells per well, treated with 10-fold dilutions of an FDA-approved oncology (FAO) drug panel, and imaged for 5 days  

HTS031.csv: Small cell lung cancer cell lines (H1048, H841, H1607, H446, H196, H69) treated with FAO and aurora kinase inhibitors and imaged for 5 days  


Column Definitions (Thunor Format)

The data follows the Vanderbilt HTS Core format used by Thunor (https://docs.thunor.net/create-a-dataset).



upid: Unique plate identifier.

well: Well position (e.g., A01).

cell.count: Nuclei count / fluorescence proxy for cell viability.

time: Time of exposure in hours.

cell.line: Cell line name.

drug1: Name of the primary drug treated.

drug1.conc: Concentration of the drug.

drug1.units: Concentration units (Molar).

expt.id: Experiment ID associated with the run.


Methodology

Cells were seeded into 384-well plates, treated with drugs at indicated concentrations, and imaged for five days (with drug replacement after 72 h) using a Molecular Devices ImageXpress Micro as described in references below. 

Fluorescence microscopy imaging described in:

Harris LA, Frick PL, Garbett SP, Hardeman KN, Paudel BB, Lopez CF, Quaranta V, Tyson DR. An unbiased metric of antiproliferative drug effect in vitro. Nat Methods. 2016; 13(6) 497-500. doi:10.1038/nmeth.3852. PubMed PMID: 27135974. PMCID: PMC4887341.

Meyer CT, Wooten DJ, Paudel BB, Bauer J, Hardeman KN, Westover D, Lovly CM, Harris LA, Tyson DR, Quaranta V. Quantifying Drug Combination Synergy along Potency and Efficacy Axes. Cell Syst. 2019; 8(2) 97-108.e16. doi:10.1016/j.cels.2019.01.003. PubMed PMID: 30797775. PMCID: PMC6675406.

Full description of the Thunor open-source software

Lubbock ALR, Harris LA, Quaranta V, Tyson DR, Lopez CF. Thunor: visualization and analysis of high-throughput dose-response datasets. Nucleic Acids Res. 2021; 49(W1) W633-W640. doi:10.1093/nar/gkab424. PubMed PMID: 34038546. PMCID: PMC8265171.  

https://docs.thunor.nethttps://github.com/alubbock/thunor-web

HTS001 and HTS003 datasets were used to support:

Harris LA, Frick PL, Garbett SP, Hardeman KN, Paudel BB, Lopez CF, Quaranta V, Tyson DR. An unbiased metric of antiproliferative drug effect in vitro. Nat Methods. 2016; 13(6) 497-500. doi:10.1038/nmeth.3852. PubMed PMID: 27135974. PMCID: PMC4887341.

Hayford CE, Tyson DR, Robbins CJ, Frick PL, Quaranta V, Harris LA. An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PLoS Biol. 2021; 19(6) e3000797. doi:10.1371/journal.pbio.3000797. PubMed PMID: 34061819. PMCID: PMC8195356.

HTS031 dataset was used to support:

Groves SM, Ildefonso GV, McAtee CO, Ozawa PMM, Ireland AS, Stauffer PE, Wasdin PT, Huang X, Qiao Y, Lim JS, Bader J, Liu Q, Simmons AJ, Lau KS, Iams WT, Hardin DP, Saff EB, Holmes WR, Tyson DR, Lovly CM, Rathmell JC, Marth G, Sage J, Oliver TG, Weaver AM, Quaranta V. Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer. Cell Syst. 2022; 13(9) 690-710.e17. doi:10.1016/j.cels.2022.07.006. PubMed PMID: 35981544. PMCID: PMC9615940.