An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay.
Bioinformatics
; 36(24): 5686-5694, 2021 Apr 05.
Article
in En
| MEDLINE
| ID: mdl-33367496
ABSTRACT
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. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2021
Type:
Article
Affiliation country:
Netherlands