Mapping the Localization of Proteins Within Filopodia Using FiloMap

Guillaume Jacquemet

doi:10.1007/978-1-0716-2887-4_4

Mapping the Localization of Proteins Within Filopodia Using FiloMap

Guillaume Jacquemet

Biokemia ja solubiologia

Tutkimustuotos: Artikkeli kirjassa/raportissa/konferenssijulkaisussa › Luku › Tieteellinen › vertaisarvioitu

3 Sitaatiot (Scopus)

12 Lataukset (Pure)

Abstrakti

Filopodia are fingerlike membrane protrusions extended by cells to sense their environment. Filopodia are widely used by migrating cells in vivo and directly contribute to several physiological processes and diseases. Due to the essential roles of filopodia in sensing the extracellular environment, there is a need to characterize their composition and ultrastructure further. This chapter highlights FiloMap, an image analysis pipeline that utilizes Fiji and R to map the localization of proteins within filopodia from microscopy images. I provide step-by-step protocols on (a) setting up FiloMap in Fiji and R, (b) extracting line intensity profiles from filopodia stainings in Fiji, (c) further analyzing line intensity profiles in R, and (d) creating filopodia maps to compare the localization of multiple proteins within filopodia. Notably, while FiloMap was written to analyze filopodia, the analysis pipeline described here can also analyze and compile any line intensity profiles.

Alkuperäiskieli	Englanti
Otsikko	Methods in Molecular Biology
Toimittajat	Coert Margadant
Kustantaja	Humana press
Sivut	51-61
Sivumäärä	11
Vuosikerta	2608
ISBN (elektroninen)	978-1-0716-2887-4
ISBN (painettu)	978-1-0716-2886-7
DOI - pysyväislinkit	https://doi.org/10.1007/978-1-0716-2887-4_4
Tila	Julkaistu - 19 tammik. 2023
OKM-julkaisutyyppi	A3 Kirjan osa tai toinen tutkimuskirja

Julkaisusarja

Nimi	Methods in Molecular Biology
Vuosikerta	2608
ISSN (painettu)	1064-3745
ISSN (elektroninen)	1940-6029

Rahoitus

I thank Sujan Ghimire, Ana Popović, and Joanna Pylv€an€ainen for helping test FiloMap. The Cell Imaging and Cytometry core facility (Turku Bioscience, University of Turku, Åbo Akademi University, and Biocenter Finland) and Turku BioImaging are acknowledged for their services, instrumentation, and expertise. This work was supported by the Academy of Finland (338537), the Sigrid Jusélius Foundation, the Finnish Heart Foundation, and the Finnish Cancer Foundation. This research was also supported by InFLAMES Flagship Programme of the Academy of Finland (decision numbers: 337531).

Pääsy asiakirjaan

10.1007/978-1-0716-2887-4_4

Mapping the localization of proteins within filopodia using FiloMap

https://urn.fi/URN:NBN:fi-fe202502018603

Viittausmuodot

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abstract = "Filopodia are fingerlike membrane protrusions extended by cells to sense their environment. Filopodia are widely used by migrating cells in vivo and directly contribute to several physiological processes and diseases. Due to the essential roles of filopodia in sensing the extracellular environment, there is a need to characterize their composition and ultrastructure further. This chapter highlights FiloMap, an image analysis pipeline that utilizes Fiji and R to map the localization of proteins within filopodia from microscopy images. I provide step-by-step protocols on (a) setting up FiloMap in Fiji and R, (b) extracting line intensity profiles from filopodia stainings in Fiji, (c) further analyzing line intensity profiles in R, and (d) creating filopodia maps to compare the localization of multiple proteins within filopodia. Notably, while FiloMap was written to analyze filopodia, the analysis pipeline described here can also analyze and compile any line intensity profiles.",

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AB - Filopodia are fingerlike membrane protrusions extended by cells to sense their environment. Filopodia are widely used by migrating cells in vivo and directly contribute to several physiological processes and diseases. Due to the essential roles of filopodia in sensing the extracellular environment, there is a need to characterize their composition and ultrastructure further. This chapter highlights FiloMap, an image analysis pipeline that utilizes Fiji and R to map the localization of proteins within filopodia from microscopy images. I provide step-by-step protocols on (a) setting up FiloMap in Fiji and R, (b) extracting line intensity profiles from filopodia stainings in Fiji, (c) further analyzing line intensity profiles in R, and (d) creating filopodia maps to compare the localization of multiple proteins within filopodia. Notably, while FiloMap was written to analyze filopodia, the analysis pipeline described here can also analyze and compile any line intensity profiles.

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KW - Proteins/metabolism

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Mapping the Localization of Proteins Within Filopodia Using FiloMap

Abstrakti

Julkaisusarja

Rahoitus

Pääsy asiakirjaan

Sormenjälki

Viittausmuodot