期刊
BIOINFORMATICS
卷 36, 期 24, 页码 5686-5694出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btaa1073
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类别
资金
- FCT-Fundacao para a Ciencia e a Tecnologia, Portugal [UIDB/04046/2020, UIDP/04046/2020]
- 'HIT-CF' from EU [H2020-SC1-2017-755021]
- FCT [SFRH/BPD/93017/2013, PPBI-POCI-01-0145-FEDER-022122]
- Dutch Cystic Fibrosis Foundation (Nederlandse Cystic Fibrosis Stichting)
- Dutch Cystic Fibrosis Foundation (HIT-CF program)
Motivation: The 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. Results: We 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. Availability and implementation: All 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. Contact: hmbotelho@fc.ul.pt Supplementary information: Supplementary data are available at Bioinformatics online.
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