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Publication details

Document type
Journal articles

Document subtype
Full paper

Title
An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Participants in the publication
Marne C Hagemeijer (Author)
University Medical Centre Utrecht
Annelotte M Vonk (Author)
University Medical Centre Utrecht
Nikhil T Awatade (Author)
BioISI - Biosystems & Integrative Sciences Institute
Iris A L Silva (Author)
BIOISI - Instituto de Biossistemas e Ciências Integrativas
Christian Tischer (Author)
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Volker Hilsenstein (Author)
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Jeffrey M Beekman (Author)
University Medical Centre Utrecht
Margarida D Amaral (Author)
BIOISI - Instituto de Biossistemas e Ciências Integrativas
Hugo M Botelho (Author)
BIOISI - Instituto de Biossistemas e Ciências Integrativas

Scope
International

Refereeing
Yes

Summary
Motivation\nThe forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility.\n\nResults\nWe developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids.\n\nAvailability and implementation\nAll workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0.\n\nSupplementary information\nSupplementary data are available at Bioinformatics online.

Date of Submisson/Request
2020-06-06
Date of Acceptance
2020-12-14
Date of Publication
2020-12-26

Where published
Bioinformatics

Publication Identifiers
ISSN - 1367-4803

Publisher
Oxford University Press (OUP)

Document Identifiers
DOI - https://doi.org/10.1093/bioinformatics/btaa1073
URL - http://dx.doi.org/10.1093/bioinformatics/btaa1073


Export

APA
Marne C Hagemeijer, Annelotte M Vonk, Nikhil T Awatade, Iris A L Silva, Christian Tischer, Volker Hilsenstein, Jeffrey M Beekman, Margarida D Amaral, Hugo M Botelho, (2020). An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay. Bioinformatics, ISSN 1367-4803. eISSN . http://dx.doi.org/10.1093/bioinformatics/btaa1073

IEEE
Marne C Hagemeijer, Annelotte M Vonk, Nikhil T Awatade, Iris A L Silva, Christian Tischer, Volker Hilsenstein, Jeffrey M Beekman, Margarida D Amaral, Hugo M Botelho, "An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay" in Bioinformatics, 2020. 10.1093/bioinformatics/btaa1073

BIBTEX
@article{49225, author = {Marne C Hagemeijer and Annelotte M Vonk and Nikhil T Awatade and Iris A L Silva and Christian Tischer and Volker Hilsenstein and Jeffrey M Beekman and Margarida D Amaral and Hugo M Botelho}, title = {An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay}, journal = {Bioinformatics}, year = 2020, }