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A microfluidic device and computational platform for high throughput live imaging of gene expression

To fully describe gene expression dynamics requires the ability to quantitatively capture expression in individual cells over time. Automated systems for acquiring and analyzing real-time images are needed to obtain unbiased data across many samples and conditions. We developed a microfluidics devic...

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Autores principales: Busch, Wolfgang, Moore, Brad T., Martsberger, Bradley, Mace, Daniel L., Twigg, Richard W., Jung, Jee, Pruteanu-Malinici, Iulian, Kennedy, Scott J., Fricke, Gregory K., Clark, Robert L., Ohler, Uwe, Benfey, Philip N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3492502/
https://www.ncbi.nlm.nih.gov/pubmed/23023597
http://dx.doi.org/10.1038/nmeth.2185
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author Busch, Wolfgang
Moore, Brad T.
Martsberger, Bradley
Mace, Daniel L.
Twigg, Richard W.
Jung, Jee
Pruteanu-Malinici, Iulian
Kennedy, Scott J.
Fricke, Gregory K.
Clark, Robert L.
Ohler, Uwe
Benfey, Philip N.
author_facet Busch, Wolfgang
Moore, Brad T.
Martsberger, Bradley
Mace, Daniel L.
Twigg, Richard W.
Jung, Jee
Pruteanu-Malinici, Iulian
Kennedy, Scott J.
Fricke, Gregory K.
Clark, Robert L.
Ohler, Uwe
Benfey, Philip N.
author_sort Busch, Wolfgang
collection PubMed
description To fully describe gene expression dynamics requires the ability to quantitatively capture expression in individual cells over time. Automated systems for acquiring and analyzing real-time images are needed to obtain unbiased data across many samples and conditions. We developed a microfluidics device, the RootArray, in which 64 Arabidopsis thaliana seedlings can be grown and their roots imaged by confocal microscopy over several days without manual intervention. To achieve high throughput, we decoupled acquisition from analysis. In the acquisition phase, we obtain images at low magnification and segment to identify regions of interest. Coordinates are communicated to the microscope to record the regions of interest at high magnification. In the analysis phase, we reconstruct 3D objects from stitched high magnification images, and extract quantitative measurements from a virtual medial section of the root. We tracked hundreds of roots to capture detailed expression patterns of 12 transgenic reporter lines under different conditions.
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spelling pubmed-34925022013-05-01 A microfluidic device and computational platform for high throughput live imaging of gene expression Busch, Wolfgang Moore, Brad T. Martsberger, Bradley Mace, Daniel L. Twigg, Richard W. Jung, Jee Pruteanu-Malinici, Iulian Kennedy, Scott J. Fricke, Gregory K. Clark, Robert L. Ohler, Uwe Benfey, Philip N. Nat Methods Article To fully describe gene expression dynamics requires the ability to quantitatively capture expression in individual cells over time. Automated systems for acquiring and analyzing real-time images are needed to obtain unbiased data across many samples and conditions. We developed a microfluidics device, the RootArray, in which 64 Arabidopsis thaliana seedlings can be grown and their roots imaged by confocal microscopy over several days without manual intervention. To achieve high throughput, we decoupled acquisition from analysis. In the acquisition phase, we obtain images at low magnification and segment to identify regions of interest. Coordinates are communicated to the microscope to record the regions of interest at high magnification. In the analysis phase, we reconstruct 3D objects from stitched high magnification images, and extract quantitative measurements from a virtual medial section of the root. We tracked hundreds of roots to capture detailed expression patterns of 12 transgenic reporter lines under different conditions. 2012-09-30 2012-11 /pmc/articles/PMC3492502/ /pubmed/23023597 http://dx.doi.org/10.1038/nmeth.2185 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Busch, Wolfgang
Moore, Brad T.
Martsberger, Bradley
Mace, Daniel L.
Twigg, Richard W.
Jung, Jee
Pruteanu-Malinici, Iulian
Kennedy, Scott J.
Fricke, Gregory K.
Clark, Robert L.
Ohler, Uwe
Benfey, Philip N.
A microfluidic device and computational platform for high throughput live imaging of gene expression
title A microfluidic device and computational platform for high throughput live imaging of gene expression
title_full A microfluidic device and computational platform for high throughput live imaging of gene expression
title_fullStr A microfluidic device and computational platform for high throughput live imaging of gene expression
title_full_unstemmed A microfluidic device and computational platform for high throughput live imaging of gene expression
title_short A microfluidic device and computational platform for high throughput live imaging of gene expression
title_sort microfluidic device and computational platform for high throughput live imaging of gene expression
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3492502/
https://www.ncbi.nlm.nih.gov/pubmed/23023597
http://dx.doi.org/10.1038/nmeth.2185
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