Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.

Understanding the function and evolution of developmental regulatory networks requires the characterisation and quantification of spatio-temporal gene expression patterns across a range of systems and species. However, most high-throughput methods to measure the dynamics of gene expression do not pr...

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Autores principales:	Anton Crombach, Damjan Cicin-Sain, Karl R Wotton, Johannes Jaeger
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c3622fb115044f5b9bcc942e3a5e3519
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id	oai:doaj.org-article:c3622fb115044f5b9bcc942e3a5e3519
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spelling	oai:doaj.org-article:c3622fb115044f5b9bcc942e3a5e35192021-11-18T08:13:36ZMedium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.1932-620310.1371/journal.pone.0046658https://doaj.org/article/c3622fb115044f5b9bcc942e3a5e35192012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23029561/?tool=EBIhttps://doaj.org/toc/1932-6203Understanding the function and evolution of developmental regulatory networks requires the characterisation and quantification of spatio-temporal gene expression patterns across a range of systems and species. However, most high-throughput methods to measure the dynamics of gene expression do not preserve the detailed spatial information needed in this context. For this reason, quantification methods based on image bioinformatics have become increasingly important over the past few years. Most available approaches in this field either focus on the detailed and accurate quantification of a small set of gene expression patterns, or attempt high-throughput analysis of spatial expression through binary pattern extraction and large-scale analysis of the resulting datasets. Here we present a robust, "medium-throughput" pipeline to process in situ hybridisation patterns from embryos of different species of flies. It bridges the gap between high-resolution, and high-throughput image processing methods, enabling us to quantify graded expression patterns along the antero-posterior axis of the embryo in an efficient and straightforward manner. Our method is based on a robust enzymatic (colorimetric) in situ hybridisation protocol and rapid data acquisition through wide-field microscopy. Data processing consists of image segmentation, profile extraction, and determination of expression domain boundary positions using a spline approximation. It results in sets of measured boundaries sorted by gene and developmental time point, which are analysed in terms of expression variability or spatio-temporal dynamics. Our method yields integrated time series of spatial gene expression, which can be used to reverse-engineer developmental gene regulatory networks across species. It is easily adaptable to other processes and species, enabling the in silico reconstitution of gene regulatory networks in a wide range of developmental contexts.Anton CrombachDamjan Cicin-SainKarl R WottonJohannes JaegerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e46658 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anton Crombach Damjan Cicin-Sain Karl R Wotton Johannes Jaeger Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.
description	Understanding the function and evolution of developmental regulatory networks requires the characterisation and quantification of spatio-temporal gene expression patterns across a range of systems and species. However, most high-throughput methods to measure the dynamics of gene expression do not preserve the detailed spatial information needed in this context. For this reason, quantification methods based on image bioinformatics have become increasingly important over the past few years. Most available approaches in this field either focus on the detailed and accurate quantification of a small set of gene expression patterns, or attempt high-throughput analysis of spatial expression through binary pattern extraction and large-scale analysis of the resulting datasets. Here we present a robust, "medium-throughput" pipeline to process in situ hybridisation patterns from embryos of different species of flies. It bridges the gap between high-resolution, and high-throughput image processing methods, enabling us to quantify graded expression patterns along the antero-posterior axis of the embryo in an efficient and straightforward manner. Our method is based on a robust enzymatic (colorimetric) in situ hybridisation protocol and rapid data acquisition through wide-field microscopy. Data processing consists of image segmentation, profile extraction, and determination of expression domain boundary positions using a spline approximation. It results in sets of measured boundaries sorted by gene and developmental time point, which are analysed in terms of expression variability or spatio-temporal dynamics. Our method yields integrated time series of spatial gene expression, which can be used to reverse-engineer developmental gene regulatory networks across species. It is easily adaptable to other processes and species, enabling the in silico reconstitution of gene regulatory networks in a wide range of developmental contexts.
format	article
author	Anton Crombach Damjan Cicin-Sain Karl R Wotton Johannes Jaeger
author_facet	Anton Crombach Damjan Cicin-Sain Karl R Wotton Johannes Jaeger
author_sort	Anton Crombach
title	Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.
title_short	Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.
title_full	Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.
title_fullStr	Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.
title_full_unstemmed	Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.
title_sort	medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/c3622fb115044f5b9bcc942e3a5e3519
work_keys_str_mv	AT antoncrombach mediumthroughputprocessingofwholemountinsituhybridisationexperimentsintogeneexpressiondomains AT damjancicinsain mediumthroughputprocessingofwholemountinsituhybridisationexperimentsintogeneexpressiondomains AT karlrwotton mediumthroughputprocessingofwholemountinsituhybridisationexperimentsintogeneexpressiondomains AT johannesjaeger mediumthroughputprocessingofwholemountinsituhybridisationexperimentsintogeneexpressiondomains
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Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains.

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