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Best practices for instrument settings and raw data analysis in plant flow cytometry
Petr Koutecký1, Tyler Smith2, João Loureiro3
1Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czechia.
Summary
Standardizing flow cytometry (FCM) methods ensures reliable plant ploidy and genome size measurements. This guide details best practices for instrument settings and data analysis in plant FCM.
Area of Science:
- Plant science
- Cytometry
Background:
- Flow cytometry (FCM) is the primary method for determining plant ploidy levels and genome size.
- Standardization and adherence to best practices are crucial for reliable and reproducible FCM measurements in plants.
Purpose of the Study:
- To provide a comprehensive overview of best practices for flow cytometry in plant science.
- To guide researchers in standardizing methodology for accurate ploidy and genome size determination.
Main Methods:
- Discussion of instrument calibration and quality control procedures.
- Detailed examination of instrument and acquisition settings (parameters, flow rate, event count, scales, discriminators, peak positions).
- Description and comparison of raw data analysis approaches: gating and histogram modeling.
Main Results:
- Instrument and acquisition settings significantly impact data quality and downstream analyses.
- Both gating and histogram modeling have distinct advantages and disadvantages for raw data analysis.
Conclusions:
- Adherence to standardized protocols for instrument settings and data analysis is essential for reproducible plant FCM.
- Implementing the recommended best practices will enhance the reliability of ploidy and genome size data in plants.
