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Time-resolved cell culture assay analyser (TReCCA Analyser) for the analysis of on-line data: data integration--sensor correction--time-resolved IC50 determination.

Lochead J, Schessner J, Werner T, Wölfl S - PLoS ONE (2015)

Bottom Line: The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points.To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin.The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html.

View Article: PubMed Central - PubMed

Affiliation: Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany; Institute for Analytical Chemistry, Mannheim University of Applied Sciences, Mannheim, Germany.

ABSTRACT
Time-resolved cell culture assays circumvent the need to set arbitrary end-points and reveal the dynamics of quality controlled experiments. However, they lead to the generation of large data sets, which can represent a complexity barrier to their use. We therefore developed the Time-Resolved Cell Culture Assay (TReCCA) Analyser program to perform standard cell assay analyses efficiently and make sophisticated in-depth analyses easily available. The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points. A time-resolved IC50/EC50 calculation provides a better understanding of drug toxicity over time and a more accurate drug to drug comparison. Finally the logarithmic sensor recalibration function, for sensors with an exponential calibration curve, homogenises the sensor output and enables the detection of low-scale changes. To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin. The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html. By introducing the program, we hope to encourage more systematic use of time-resolved assays and lead researchers to fully exploit their data.

No MeSH data available.


Related in: MedlinePlus

TReCCA Analyser user interface and analysis steps.Consecutive tabs are clicked through for data analysis and plotting. These include the “Analysis options” tab (A), where the analyses to be performed on the data are selected and their corresponding parameters entered, and the “Graph output” tab (B), where the graphs are visualised and can be further customised. These tabs can be seen at a higher resolution in S1 and S2 Figs. All the analysis steps are summarised in the program flow chart (C). The black rectangle encloses a more precise representation of the available analysis options. The black arrows depict the succession of steps that are performed in our example of the analysis of the effect of Cisplatin on MCF-7 cells, the coloured arrows depict alternative analysis flows.
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pone.0131233.g001: TReCCA Analyser user interface and analysis steps.Consecutive tabs are clicked through for data analysis and plotting. These include the “Analysis options” tab (A), where the analyses to be performed on the data are selected and their corresponding parameters entered, and the “Graph output” tab (B), where the graphs are visualised and can be further customised. These tabs can be seen at a higher resolution in S1 and S2 Figs. All the analysis steps are summarised in the program flow chart (C). The black rectangle encloses a more precise representation of the available analysis options. The black arrows depict the succession of steps that are performed in our example of the analysis of the effect of Cisplatin on MCF-7 cells, the coloured arrows depict alternative analysis flows.

Mentions: Particular effort was put in designing a friendly user interface for the TReCCA Analyser. It was improved after being tested by 25 users for intuitiveness, clarity, and speed. Two screen shots of different tabs of the user interface, the “Analysis options” tab and the “Graph output” tab, are displayed in Fig 1A and 1B respectively.


Time-resolved cell culture assay analyser (TReCCA Analyser) for the analysis of on-line data: data integration--sensor correction--time-resolved IC50 determination.

Lochead J, Schessner J, Werner T, Wölfl S - PLoS ONE (2015)

TReCCA Analyser user interface and analysis steps.Consecutive tabs are clicked through for data analysis and plotting. These include the “Analysis options” tab (A), where the analyses to be performed on the data are selected and their corresponding parameters entered, and the “Graph output” tab (B), where the graphs are visualised and can be further customised. These tabs can be seen at a higher resolution in S1 and S2 Figs. All the analysis steps are summarised in the program flow chart (C). The black rectangle encloses a more precise representation of the available analysis options. The black arrows depict the succession of steps that are performed in our example of the analysis of the effect of Cisplatin on MCF-7 cells, the coloured arrows depict alternative analysis flows.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482264&req=5

pone.0131233.g001: TReCCA Analyser user interface and analysis steps.Consecutive tabs are clicked through for data analysis and plotting. These include the “Analysis options” tab (A), where the analyses to be performed on the data are selected and their corresponding parameters entered, and the “Graph output” tab (B), where the graphs are visualised and can be further customised. These tabs can be seen at a higher resolution in S1 and S2 Figs. All the analysis steps are summarised in the program flow chart (C). The black rectangle encloses a more precise representation of the available analysis options. The black arrows depict the succession of steps that are performed in our example of the analysis of the effect of Cisplatin on MCF-7 cells, the coloured arrows depict alternative analysis flows.
Mentions: Particular effort was put in designing a friendly user interface for the TReCCA Analyser. It was improved after being tested by 25 users for intuitiveness, clarity, and speed. Two screen shots of different tabs of the user interface, the “Analysis options” tab and the “Graph output” tab, are displayed in Fig 1A and 1B respectively.

Bottom Line: The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points.To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin.The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html.

View Article: PubMed Central - PubMed

Affiliation: Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany; Institute for Analytical Chemistry, Mannheim University of Applied Sciences, Mannheim, Germany.

ABSTRACT
Time-resolved cell culture assays circumvent the need to set arbitrary end-points and reveal the dynamics of quality controlled experiments. However, they lead to the generation of large data sets, which can represent a complexity barrier to their use. We therefore developed the Time-Resolved Cell Culture Assay (TReCCA) Analyser program to perform standard cell assay analyses efficiently and make sophisticated in-depth analyses easily available. The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points. A time-resolved IC50/EC50 calculation provides a better understanding of drug toxicity over time and a more accurate drug to drug comparison. Finally the logarithmic sensor recalibration function, for sensors with an exponential calibration curve, homogenises the sensor output and enables the detection of low-scale changes. To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin. The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html. By introducing the program, we hope to encourage more systematic use of time-resolved assays and lead researchers to fully exploit their data.

No MeSH data available.


Related in: MedlinePlus