Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS
Fluorescence time-lapse microscopy has become a powerful tool in the study of many biological processes at the single-cell level. In particular, movies depicting the temporal dependence of gene expression provide insight into the dynamics of its regulation; however, there are many technical challeng...
| Main Authors: | , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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MyJoVE Corporation
2014
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| Online Access: | http://hdl.handle.net/1721.1/89640 |
| _version_ | 1826190438128680960 |
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| author | Zopf, Christopher J. Maheshri, Narendra |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Zopf, Christopher J. Maheshri, Narendra |
| author_sort | Zopf, Christopher J. |
| collection | MIT |
| description | Fluorescence time-lapse microscopy has become a powerful tool in the study of many biological processes at the single-cell level. In particular, movies depicting the temporal dependence of gene expression provide insight into the dynamics of its regulation; however, there are many technical challenges to obtaining and analyzing fluorescence movies of single cells. We describe here a simple protocol using a commercially available microfluidic culture device to generate such data, and a MATLAB-based, graphical user interface (GUI) -based software package to quantify the fluorescence images. The software segments and tracks cells, enables the user to visually curate errors in the data, and automatically assigns lineage and division times. The GUI further analyzes the time series to produce whole cell traces as well as their first and second time derivatives. While the software was designed for S. cerevisiae, its modularity and versatility should allow it to serve as a platform for studying other cell types with few modifications. |
| first_indexed | 2024-09-23T08:40:15Z |
| format | Article |
| id | mit-1721.1/89640 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T08:40:15Z |
| publishDate | 2014 |
| publisher | MyJoVE Corporation |
| record_format | dspace |
| spelling | mit-1721.1/896402022-09-30T10:22:28Z Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS Zopf, Christopher J. Maheshri, Narendra Massachusetts Institute of Technology. Department of Chemical Engineering Zopf, Christopher J. Maheshri, Narendra Fluorescence time-lapse microscopy has become a powerful tool in the study of many biological processes at the single-cell level. In particular, movies depicting the temporal dependence of gene expression provide insight into the dynamics of its regulation; however, there are many technical challenges to obtaining and analyzing fluorescence movies of single cells. We describe here a simple protocol using a commercially available microfluidic culture device to generate such data, and a MATLAB-based, graphical user interface (GUI) -based software package to quantify the fluorescence images. The software segments and tracks cells, enables the user to visually curate errors in the data, and automatically assigns lineage and division times. The GUI further analyzes the time series to produce whole cell traces as well as their first and second time derivatives. While the software was designed for S. cerevisiae, its modularity and versatility should allow it to serve as a platform for studying other cell types with few modifications. Massachusetts Institute of Technology (Startup funds) National Institutes of Health (U.S.) (grant GM95733) 2014-09-15T20:47:44Z 2014-09-15T20:47:44Z 2013-07 Article http://purl.org/eprint/type/JournalArticle 1940-087X http://hdl.handle.net/1721.1/89640 Zopf, Christopher J., and Narendra Maheshri. “Acquiring Fluorescence Time-Lapse Movies of Budding Yeast and Analyzing Single-Cell Dynamics Using GRAFTS.” JoVE no. 77 (2013). en_US http://dx.doi.org/10.3791/50456 Journal of Visualized Experiments Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf MyJoVE Corporation MyJoVE Corporation |
| spellingShingle | Zopf, Christopher J. Maheshri, Narendra Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS |
| title | Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS |
| title_full | Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS |
| title_fullStr | Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS |
| title_full_unstemmed | Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS |
| title_short | Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS |
| title_sort | acquiring fluorescence time lapse movies of budding yeast and analyzing single cell dynamics using grafts |
| url | http://hdl.handle.net/1721.1/89640 |
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