Login

Notice: Temporary Suspension of New Experiment Creation
We have temporarily disabled the creation of new experiments as we are continuously running out of space. This issue has been impacting both uploads and downloads from FlowRepository. By taking this step, we aim to make downloads of existing data more reliable.
We apologize for the inconvenience and appreciate your understanding as we work on upgrading our hardware and improving the overall solution.
Thank you for your patience.

Download-button_s

Experiment Overview

Repository ID: FR-FCM-Z2CJ Experiment name: Bacterial mock communities as standards for reproducible cytometric microbiome analysis MIFlowCyt score: 86.22%
Primary researcher: nicolas cichocki PI/manager: Florian Schattenberg Uploaded by: nicolas cichocki
Experiment dates: 2017-05-01 - 2019-12-14 Dataset uploaded: Nov 2019 Last updated: Sep 2021
Keywords: [microbial flow cytometry] [single cell analysis] [microbial Cytometric Mock Community (mCMC)] [microbial community assembly] [flow cytometric standards] Manuscripts:
Organizations: Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Leipzig, (Germany)
Purpose: Standards help to verify lab-workflows and ensure consistency of produced and processed data. In the present study, we introduce a suitable standard for the analysis of microbial communities by flow cytometry. Flow cytometry has become an essential technology for the quantitative study of natural or artificially-constructed microbial communities in ecosystems, biotechnology, and health research. De Vrieze et al. highlighted the need for phenotypic microbial community data in the field of biotechnology for the upcoming automation process in Industry 4.0. In addition, research only begins to uncover the ecology of microbial communities in managed and natural systems. Therefore, the technology is especially useful for monitoring dynamics and evolution of communities; and bioinformatics tools are available to identify ecological concepts of community structuring processes and to reveal stability properties4 as well as interactions between subpopulations of microorganisms and their environment. Such applications require absolute comparability of the cytometric data over days up to years. A standard mock community has been developed that validates accurate cell treatment, tests high-resolution cytometer alignment, and ensures proper use of bioinformatics pipelines.
Conclusion: Here, we developed an artificial microbial Cytometric Mock Community (mCMC) as a reference standard and benchmark for high quality data. Our approach supports quantitative assessments and qualified decisions for sorting of subcommunities suitable for subsequent high resolution sequencing or proteomic routines.
Comments: None
Funding: This work was funded by the Central Innovation Programme for SMEs (ZIM) of the Federal Ministry of Economic Affairs and Energy Germany (BMWi) (INAR-ABOS,16KN043222), the European Regional Development Funds (EFRE—Europe Funds Saxony, grant 100192205) and the Helmholtz Association within RP Renewable Energies.
Quality control: Characterizing microbiome dynamics - Flow cytometry based workflows from pure cultures to natural communities Reference beads blue 1 µm BB Fluoresbrite Microspheres (17458; Polysciences) Reference beads blue 0.5 µm BB Fluoresbrite Microspheres (18339; Polysciences) Reference beads yellow-green 1 µm FluoSpheres (F-13081, Lot 03B2-1; ThermoFischer Scientific) Reference beads yellow-green 0.5 µm FluoSpheres (F-8813, Lot. 69B3-1; ThermoFischer Scientific) Laser alignment beads blue 1 µm FluoSpheres (F-8815; ThermoFisher Scientific) Laser alignment beads yellow-green 2 µm FluoSpheres (F8827; ThermoFisher Scientific) Laser alignment BD FACSuiteTM CS&T research beads (650621; Becton, Dickinson and Company) Laser alignment BD CS&T RUO beads (661414; Becton, Dickinson and Company) Daily laser alignment. Use of mCMC as biological standards.
Download FCS Files or login and see the dataset in your inbox for further annotation details.