Preprint: Please note that this article has not completed peer review.

High-Throughput Screening Model to Quantify Re-Epithelialization Kinetics

Marcela M. Fernandez-Gutierrez, Peter P. J. Roosjen, David B. H. van Zessen, Jerry M. Wells, Peter van Baarlen, Andrew P. Stubbs, Michiel Kleerebezem
DOI: 10.1038/protex.2019.015

Abstract

In vitro scratch assays provide an attractive method to study the regulation and mechanisms of epithelial cell proliferation and migration that are involved in wound repair. The assay is performed by introducing a scratch into a confluent cell monolayer and monitoring the re-epithelialization of the “wound” by acquiring images over time. Despite improvements to the method over the past years, high-throughput screenings often require the integration of multiple image analysis and data extraction software tools. We developed a high-throughput image-based scratch assay and an automated processing pipeline that employs a mathematical model to describe re-epithelialization kinetics. We implemented a processing pipeline in Galaxy called KREAP that provides an open source web-based platform to enable scientists from diverse backgrounds to perform reproducible and quantitative repair data analyses in less than 45 minutes.

Keywords
Scratch assay, image analysis, high-throughput, re-epithelialization, cell migration, modeling, microscopy

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References

Acknowledgements

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Posted 24 Jun, 2019

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    Comments (2)

    Weijie Chen
    commented on 02 July 2019

    Did you try to publish on nature protocol? because I think it's a very good protocol.

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    Marcela Fernandez
    replied on 23 July 2019

    Dear Weijie Chen, thanks for your compliment. We did try to publish it in Nature Protocols, but the associated publications were still too recent, so the editors were still concerned about the extent of its applications.

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    Preprint: Please note that this article has not completed peer review.

    High-Throughput Screening Model to Quantify Re-Epithelialization Kinetics

    Marcela M. Fernandez-Gutierrez, Peter P. J. Roosjen, David B. H. van Zessen, Jerry M. Wells, Peter van Baarlen, Andrew P. Stubbs, Michiel Kleerebezem

    STATUS: Posted

    Comments: 2
    PDF Downloads: 0
    HTML Views: 73
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    Abstract

    In vitro scratch assays provide an attractive method to study the regulation and mechanisms of epithelial cell proliferation and migration that are involved in wound repair. The assay is performed by introducing a scratch into a confluent cell monolayer and monitoring the re-epithelialization of the “wound” by acquiring images over time. Despite improvements to the method over the past years, high-throughput screenings often require the integration of multiple image analysis and data extraction software tools. We developed a high-throughput image-based scratch assay and an automated processing pipeline that employs a mathematical model to describe re-epithelialization kinetics. We implemented a processing pipeline in Galaxy called KREAP that provides an open source web-based platform to enable scientists from diverse backgrounds to perform reproducible and quantitative repair data analyses in less than 45 minutes.

    Figures

    Introduction

    Reagents

    Equipment

    Procedure

    Timing

    Troubleshooting

    Anticipated Results

    References

    Acknowledgements

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