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Experiment Overview

Repository ID: FR-FCM-ZZP6 Experiment name: Flow Cytometric Analysis of Murine Microbiota in T Cell Transfer Colitis 1 MIFlowCyt score: 92.67%
Primary researcher: Jakob Zimmermann PI/manager: Hyun-Dong Chang Uploaded by: Jakob Zimmermann
Experiment dates: 2013-11-12 - 2014-07-09 Dataset uploaded: Feb 2016 Last updated: Feb 2016
Keywords: [flow cytometry] [microbial communities] [Microbiota] [colitis] Manuscripts: [26909672] Eurojimmunollogo
Organizations: German Rheumatism Research Center Berlin, Cell Biology Group, Berlin, (Germany)
Helmholtz Center for Environmental Research, Environmental Microbiology, Leipzig, (Germany)
Purpose: In recent years, high-resolution analysis of bacterial forward scatter and DNA content by flow cytometry has enabled the near-realtime analysis of dynamic changes in the composition of complex bacterial ecosystems (Koch C et al., Nature Protocols, 2013). We sought to apply this method to detect changes in the composition of the fecal microbiota in mice in the course of experimentally induced inflammation of the colon.
Conclusion: Measuring bacterial forward scatter and DNA content, we were able to discriminate up to 80 sub-populations in fecal microbiomes of mice before and after the onset of colitis. Our method identified dramatic differences in the composition of the fecal microbiota in colitis compared to healthy mice.
Comments: None
Funding: This work was supported by the German Research Council (DFG SFB 633, SFB 650, SPP 1656, and GRK1121) and the European Research Council advanced grant ERC-2010-AdG_20100317 Grant 268987. The DRFZ is a Leibniz institute.
Quality control: Fluorescent beads FluoSpheres 2 µm (505/515, Lot-Nr. 24498W, Molecular Probes Eugene, Oregon, USA), FluoSpheres 1 µm (350/440, Lot-Nr. 69A1-1, Molecular Probes Eugene, Oregon, USA), and Fluoresbrite BB Carboxylate microspheres 0.5 µm (360/407, Lot-Nr. 552744, Polyscience, USA) were used to align the instrumental settings.


Experiment variables

Timepoints
· 0 112-2_d0.fcs · 112-3_d0.fcs · 113-2_d0.fcs · 113-3_d0.fcs · 94-1_d0.fcs · 94-2_d0.fcs · 97-1_d0.fcs · 97-2_d0.fcs · Healthy_01.fcs · Healthy_02.fcs · Healthy_03.fcs · Healthy_04.fcs
· 6 112-2_d6.fcs · 112-3_d6.fcs · 113-2_d6.fcs · 113-3_d6.fcs
· 8 112-2_d8.fcs · 112-3_d8.fcs · 113-2_d8.fcs · 113-3_d8.fcs
· 10 112-3_d10.fcs · 113-2_d10.fcs · 113-3_d10.fcs
· 15 112-2_d15.fcs · 112-3_d15.fcs · 113-3_d15.fcs · Wt_01.fcs · Wt_02.fcs · Wt_03.fcs · Wt_04.fcs
· 3 94-1_d3.fcs · 94-2_d3.fcs · 97-1_d3.fcs · 97-2_d3.fcs
· 5 94-1_d5.fcs · 94-2_d5.fcs · 97-1_d5.fcs · 97-2_d5.fcs
· 7 94-1_d7.fcs · 94-2_d7.fcs · 97-1_d7.fcs · 97-2_d7.fcs
· 9 94-1_d9.fcs · 94-2_d9.fcs · 97-1_d9.fcs · 97-2_d9.fcs
· 11 94-1_d11.fcs · 94-2_d11.fcs · 97-1_d11.fcs · 97-2_d11.fcs
· 12 94-1_d12.fcs · 94-2_d12.fcs · 97-1_d12.fcs · 97-2_d12.fcs
· 4 112-2_d4.fcs · 112-3_d4.fcs · 113-2_d4.fcs · 113-3_d4.fcs

Conditions
· healthy 112-2_d0.fcs · 112-3_d0.fcs · 113-2_d0.fcs · 113-3_d0.fcs · 94-1_d0.fcs · 94-2_d0.fcs · 97-1_d0.fcs · 97-2_d0.fcs · Healthy_01.fcs · Healthy_02.fcs · Healthy_03.fcs · Healthy_04.fcs
· colitis 112-2_d15.fcs · 112-2_d4.fcs · 112-2_d6.fcs · 112-2_d8.fcs · 112-3_d10.fcs · 112-3_d15.fcs · 112-3_d4.fcs · 112-3_d6.fcs · 112-3_d8.fcs · 113-2_d10.fcs · 113-2_d4.fcs · 113-2_d6.fcs · 113-2_d8.fcs · 113-3_d10.fcs · 113-3_d15.fcs · 113-3_d4.fcs · 113-3_d6.fcs · 113-3_d8.fcs · 94-1_d11.fcs · 94-1_d12.fcs · 94-1_d3.fcs · 94-1_d5.fcs · 94-1_d7.fcs · 94-1_d9.fcs · 94-2_d11.fcs · 94-2_d12.fcs · 94-2_d3.fcs · 94-2_d5.fcs · 94-2_d7.fcs · 94-2_d9.fcs · 97-1_d11.fcs · 97-1_d12.fcs · 97-1_d3.fcs · 97-1_d5.fcs · 97-1_d7.fcs · 97-1_d9.fcs · 97-2_d11.fcs · 97-2_d12.fcs · 97-2_d3.fcs · 97-2_d5.fcs · 97-2_d7.fcs · 97-2_d9.fcs · Wt_01.fcs · Wt_02.fcs · Wt_03.fcs · Wt_04.fcs

Individuals
· 94-1 94-1_d0.fcs · 94-1_d11.fcs · 94-1_d12.fcs · 94-1_d3.fcs · 94-1_d5.fcs · 94-1_d7.fcs · 94-1_d9.fcs
· 94-2 94-2_d0.fcs · 94-2_d11.fcs · 94-2_d12.fcs · 94-2_d3.fcs · 94-2_d5.fcs · 94-2_d7.fcs · 94-2_d9.fcs
· 97-1 97-1_d0.fcs · 97-1_d11.fcs · 97-1_d12.fcs · 97-1_d3.fcs · 97-1_d5.fcs · 97-1_d7.fcs · 97-1_d9.fcs
· 97-2 97-2_d0.fcs · 97-2_d11.fcs · 97-2_d12.fcs · 97-2_d3.fcs · 97-2_d5.fcs · 97-2_d7.fcs · 97-2_d9.fcs
· 112-2 112-2_d0.fcs · 112-2_d15.fcs · 112-2_d4.fcs · 112-2_d6.fcs · 112-2_d8.fcs
· 112-3 112-3_d0.fcs · 112-3_d10.fcs · 112-3_d15.fcs · 112-3_d4.fcs · 112-3_d6.fcs · 112-3_d8.fcs
· 113-2 113-2_d0.fcs · 113-2_d10.fcs · 113-2_d4.fcs · 113-2_d6.fcs · 113-2_d8.fcs
· 113-3 113-3_d0.fcs · 113-3_d10.fcs · 113-3_d15.fcs · 113-3_d4.fcs · 113-3_d6.fcs · 113-3_d8.fcs
· 01 Healthy_01.fcs · Wt_01.fcs
· 02 Healthy_02.fcs · Wt_02.fcs
· 03 Healthy_03.fcs · Wt_03.fcs
· 04 Healthy_04.fcs · Wt_04.fcs

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