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
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)
Dep. Química e Bioquímica
BioISI
Hugo M Botelho (Author)
Dep. Química e Bioquímica
BioISI
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
Rankings
SCIMAGO Q1 (2020) - 3.599 - Biochemistry
SCIMAGO Q1 (2020) - 3.599 - Molecular Biology
SCIMAGO Q1 (2020) - 3.599 - Computer Science Applications
Web Of Science Q1 (2020) - 6.937 - BIOTECHNOLOGY & APPLIED MICROBIOLOGY - SCIE
SCIMAGO Q1 (2020) - 3.599 - Biochemistry
SCIMAGO Q1 (2020) - 3.599 - Molecular Biology