MiSet RFC Standards: Defining a Universal Minimum Set of Standards Required for Reproducibility and Rigor in Research Flow Cytometry Experiments

Abstract

Poor adherence to best practices, insufficient training, and pressure to produce data quickly may lead to publications of suboptimal biomedical research flow cytometry data, which contributes to the body of irreproducible research findings. In addition, documentation of compliance with best flow cytometry practices for submission, visualization, and publication of flow cytometry data is currently endorsed by very few scientific journals, which is particularly concerning as numerous peer-reviewed flow cytometry publications emphasize instrumentation, experimental design, and data analysis as important sources of variability. Guidelines and resources for adequate reporting, annotation and deposition of flow cytometry experiments are provided by MIFlowCyt and the FlowRepository database, and comprehensive expert recommendations covering principles and techniques of field-specific flow cytometry applications have been published. To facilitate the integration of quality-defining parameters into manuscript and grant submission and publication requirements across biomedical fields that rely on the use of flow-cytometry-based techniques, a single comprehensive yet easily and universally applicable document is needed. To produce such a list of gold-standard parameters that assess whether a research flow cytometry experiment has been planned, conducted, interpreted, and reported at the highest standard, a new initiative defining the minimum set of standards a robust and rigorous research flow experiment must fulfill (MiSet RFC Standards) was proposed at CYTO 2019. MiSet RFC Standards will integrate and simplify existing resources to provide a universal benchmark a flow cytometry experiment can easily be measured against. The goal of MiSET RFC Standards is its integration into peerreview and publication procedures through partnership with stakeholders, journals and publishers in biomedical and translational research. This article introduces the aims and anticipated timeline and discusses strategies for interdisciplinary consensus and implementation. A single-resource broadly applicable guideline will harmonize standards across different fields of biomedical research and lead to publication of more robust research findings.

Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition)

“…As of today, 39 standards are listed in the MIBBI project (https://fairsharing.org/collection/MIBBI) and a few of them are concerning immunological experiments. Table 1 and [31,32,35–40] provide examples of immunology‐related Minimal Information standards.…”

A literature study and public survey on mass cytometry dataset release and reuse

“…Similar to MIAME [9] or MINSEQE (http://fged.org/projects/ minseqe/) standards for documentation of microarray and RNAseq data, respectively, MiFlowCyt [10] and MiSet RFC [11] provide documentation standards for cytometry data. The information required by these standards could be fulfilled via specific forms during data upload (e.g., FlowRepository) or in less formal ways through spreadsheets and other files attached to the accession containing the FCS files if not directly supported by a particular repository.…”

Acquisition of murine splenic myeloid cells for protein and gene expression profiling by advanced flow cytometry and CITE-seq

“…Acquisition of a complete set of FMO controls is laborious but will aid confident discrimination of positive and negative signals. We urge new flow cytometry users to study the current literature regarding advanced flow cytometry methodology guidelines ( Mair and Tyznik, 2019 ) and recommended guidelines for flow cytometry reporting in detail ( Lucas et al., 2020 ; Cossarizza et al., 2019 ), and advise that this is not a trivial methodology.…”