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LiveFly: A Toolbox for the Analysis of Transcription Dynamics in Live Drosophila Embryos

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Morphogen Gradients

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1863))

Abstract

We present the LiveFly toolbox for quantitative analysis of transcription dynamics in live Drosophila embryos. The toolbox allows users to process two-color 3D confocal movies acquired using nuclei-labeling and the fluorescent RNA-tagging system described in the previous chapter and export the nuclei’s position as a function of time, their lineages and the intensity traces of the active loci. The toolbox, which is tailored for the context of Drosophila early development, is semiautomatic, and requires minimal user intervention. It also includes a tool to combine data from multiple movies and visualize several features of the intensity traces and the expression pattern.

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Acknowledgments

This work was supported by a Marie Curie MCCIG grant No. 303561 (AMW), PSL IDEX REFLEX (ND, AMW, MC), ANR-11-LABX-0044 DEEP Labex (ND), ANR- 11-BSV2-0024 Axomorph (ND and AMW), and PSL ANR-10-IDEX-0001-02. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Author notes

  1. Mathieu Coppey and Aleksandra M. Walczak contributed equally to this work.

Authors and Affiliations

  1. Ecole Normale Supérieure, PSL Research University, CNRS, Sorbonne Université, Laboratoire de Physique Théorique, Paris, France

    Huy Tran, Teresa Ferraro & Aleksandra M. Walczak

  2. Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics, Paris, France

    Huy Tran, Carmina Angelica Perez-Romero, Cécile Fradin & Nathalie Dostatni

  3. McMaster University, Hamilton, ON, Canada

    Carmina Angelica Perez-Romero & Cécile Fradin

  4. Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Developmental Biology, Paris, France

    Teresa Ferraro

  5. Institut Curie, PSL Research University, CNRS, Sorbonne Université, Physico Chimie, Paris, France

    Mathieu Coppey

Authors
  1. Huy Tran
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  2. Carmina Angelica Perez-Romero
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  3. Teresa Ferraro
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  4. Cécile Fradin
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  5. Nathalie Dostatni
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  6. Mathieu Coppey
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  7. Aleksandra M. Walczak
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Corresponding author

Correspondence to Aleksandra M. Walczak .

Editor information

Editors and Affiliations

  1. Integrated Microscopy Core, Baylor College of Medicine, Houston, TX, USA

    Julien Dubrulle

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Tran, H. et al. (2018). LiveFly: A Toolbox for the Analysis of Transcription Dynamics in Live Drosophila Embryos. In: Dubrulle, J. (eds) Morphogen Gradients. Methods in Molecular Biology, vol 1863. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8772-6_11

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  • DOI: https://doi.org/10.1007/978-1-4939-8772-6_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8771-9

  • Online ISBN: 978-1-4939-8772-6

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