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Experiment Overview

Repository ID: FR-FCM-Z5L7 Experiment name: Signaling pathways analysis after azithromycin exposure MIFlowCyt score: 84.00%
Primary researcher: David Michonneau PI/manager: David Michonneau Uploaded by: David Michonneau
Experiment dates: 2022-03-14 - 2022-07-12 Dataset uploaded: Jul 2022 Last updated: Aug 2022
Keywords: [human PBMCs] [CyTOF; mass cytometry; flow cytometry; standardization] [antibiotic] [azithromycin] Manuscripts: [35984904]
Organizations: INSERM U976, Human immunology, pathophysiology and immunotherapy, Paris, (France)
Purpose: Azithromycin exposure is associated with loss of T cells function, impaired glycolysis and oxidative respiration after CD3/CD28 activation. This experiment explore signaling pathways of PBMC following CD3/CD28 activation.
Conclusion: Azithromycin impairs TCR signaling pathways. Paper in Blood: 10.1182/blood.2022016926
Comments: Source code of analyses is available on a Git repository: https://gitlab.com/nivall/azimut-in-vitro
Funding: This work was funding by the Association Leucémie Espoir, SOS oxygène, La Laurène, EGMOS association, HTC Project.
Quality control: FCS files obtained after acquisition were normalized following the bead-based procedure. Identification of singlets and removal of normalization beads was performed on omiq.ai. Retrieved events were debarcoded using R CATALYST package then stored in new FCS files for further analyses. These files are uploaded in this repository.


Experiment variables

Conditions
· DMSO 20220519_C48_CD3_CD28_Processed_T0_DMSO.fcs · 20220519_C48_CD3_CD28_Processed_T1_DMSO.fcs · 20220519_C48_CD3_CD28_Processed_T2_DMSO.fcs · 20220519_C48_CD3_CD28_Processed_T3_DMSO.fcs · 20220519_C48_CD3_CD28_Processed_T4_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T0_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T1_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T2_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T3_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T4_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T0_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T1_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T2_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T3_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T4_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T0_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T1_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T2_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T3_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T4_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T0_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T1_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T2_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T3_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T4_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T4_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T4_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T4_DMSO.fcs
· AZM 20220519_C48_CD3_CD28_Processed_T0_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T1_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T2_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T3_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T4_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T0_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T1_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T2_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T3_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T4_AZM.fcs · 20220630_51_1_Processed_Concatenated_T0_AZM.fcs · 20220630_51_1_Processed_Concatenated_T1_AZM.fcs · 20220630_51_1_Processed_Concatenated_T2_AZM.fcs · 20220630_51_1_Processed_Concatenated_T3_AZM.fcs · 20220630_51_1_Processed_Concatenated_T4_AZM.fcs · 20220630_52_1_Processed_Concatenated_T0_AZM.fcs · 20220630_52_1_Processed_Concatenated_T1_AZM.fcs · 20220630_52_1_Processed_Concatenated_T2_AZM.fcs · 20220630_52_1_Processed_Concatenated_T3_AZM.fcs · 20220630_52_1_Processed_Concatenated_T4_AZM.fcs · 20220701_54_1_Processed_Concatenated_T0_AZM.fcs · 20220701_54_1_Processed_Concatenated_T1_AZM.fcs · 20220701_54_1_Processed_Concatenated_T2_AZM.fcs · 20220701_54_1_Processed_Concatenated_T3_AZM.fcs · 20220701_54_1_Processed_Concatenated_T4_AZM.fcs · 20220713_45_1_Processed_Concatenated_T0_AZM.fcs · 20220713_45_1_Processed_Concatenated_T1_AZM.fcs · 20220713_45_1_Processed_Concatenated_T2_AZM.fcs · 20220713_45_1_Processed_Concatenated_T3_AZM.fcs · 20220713_45_1_Processed_Concatenated_T4_AZM.fcs · 20220713_55_1_Processed_Concatenated_T0_AZM.fcs · 20220713_55_1_Processed_Concatenated_T1_AZM.fcs · 20220713_55_1_Processed_Concatenated_T2_AZM.fcs · 20220713_55_1_Processed_Concatenated_T3_AZM.fcs · 20220713_55_1_Processed_Concatenated_T4_AZM.fcs · 20220713_56_1_Processed_Concatenated_T0_AZM.fcs · 20220713_56_1_Processed_Concatenated_T1_AZM.fcs · 20220713_56_1_Processed_Concatenated_T2_AZM.fcs · 20220713_56_1_Processed_Concatenated_T3_AZM.fcs · 20220713_56_1_Processed_Concatenated_T4_AZM.fcs

Timepoints
· T0 20220519_C48_CD3_CD28_Processed_T0_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T0_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T0_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T0_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T0_AZM.fcs · 20220630_51_1_Processed_Concatenated_T0_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T0_AZM.fcs · 20220630_52_1_Processed_Concatenated_T0_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T0_AZM.fcs · 20220701_54_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T0_AZM.fcs · 20220713_45_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T0_AZM.fcs · 20220713_55_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T0_AZM.fcs · 20220713_56_1_Processed_Concatenated_T0_DMSO.fcs
· T1 20220519_C48_CD3_CD28_Processed_T1_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T1_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T1_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T1_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T1_AZM.fcs · 20220630_51_1_Processed_Concatenated_T1_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T1_AZM.fcs · 20220630_52_1_Processed_Concatenated_T1_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T1_AZM.fcs · 20220701_54_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T1_AZM.fcs · 20220713_45_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T1_AZM.fcs · 20220713_55_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T1_AZM.fcs · 20220713_56_1_Processed_Concatenated_T1_DMSO.fcs
· T2 20220519_C48_CD3_CD28_Processed_T2_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T2_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T2_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T2_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T2_AZM.fcs · 20220630_51_1_Processed_Concatenated_T2_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T2_AZM.fcs · 20220630_52_1_Processed_Concatenated_T2_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T2_AZM.fcs · 20220701_54_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T2_AZM.fcs · 20220713_45_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T2_AZM.fcs · 20220713_55_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T2_AZM.fcs · 20220713_56_1_Processed_Concatenated_T2_DMSO.fcs
· T3 20220519_C48_CD3_CD28_Processed_T3_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T3_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T3_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T3_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T3_AZM.fcs · 20220630_51_1_Processed_Concatenated_T3_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T3_AZM.fcs · 20220630_52_1_Processed_Concatenated_T3_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T3_AZM.fcs · 20220701_54_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T3_AZM.fcs · 20220713_45_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T3_AZM.fcs · 20220713_55_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T3_AZM.fcs · 20220713_56_1_Processed_Concatenated_T3_DMSO.fcs
· T4 20220519_C48_CD3_CD28_Processed_T4_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T4_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T4_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T4_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T4_AZM.fcs · 20220630_51_1_Processed_Concatenated_T4_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T4_AZM.fcs · 20220630_52_1_Processed_Concatenated_T4_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T4_AZM.fcs · 20220701_54_1_Processed_Concatenated_T4_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T4_AZM.fcs · 20220713_45_1_Processed_Concatenated_T4_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T4_AZM.fcs · 20220713_55_1_Processed_Concatenated_T4_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T4_AZM.fcs · 20220713_56_1_Processed_Concatenated_T4_DMSO.fcs

Individuals
· 48 20220519_C48_CD3_CD28_Processed_T0_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T0_DMSO.fcs · 20220519_C48_CD3_CD28_Processed_T1_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T1_DMSO.fcs · 20220519_C48_CD3_CD28_Processed_T2_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T2_DMSO.fcs · 20220519_C48_CD3_CD28_Processed_T3_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T3_DMSO.fcs · 20220519_C48_CD3_CD28_Processed_T4_AZM.fcs · 20220519_C48_CD3_CD28_Processed_T4_DMSO.fcs
· 49 20220519_C49_CD3_CD28_Processed_T0_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T0_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T1_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T1_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T2_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T2_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T3_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T3_DMSO.fcs · 20220519_C49_CD3_CD28_Processed_T4_AZM.fcs · 20220519_C49_CD3_CD28_Processed_T4_DMSO.fcs
· 51 20220630_51_1_Processed_Concatenated_T0_AZM.fcs · 20220630_51_1_Processed_Concatenated_T0_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T1_AZM.fcs · 20220630_51_1_Processed_Concatenated_T1_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T2_AZM.fcs · 20220630_51_1_Processed_Concatenated_T2_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T3_AZM.fcs · 20220630_51_1_Processed_Concatenated_T3_DMSO.fcs · 20220630_51_1_Processed_Concatenated_T4_AZM.fcs · 20220630_51_1_Processed_Concatenated_T4_DMSO.fcs
· 52 20220630_52_1_Processed_Concatenated_T0_AZM.fcs · 20220630_52_1_Processed_Concatenated_T0_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T1_AZM.fcs · 20220630_52_1_Processed_Concatenated_T1_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T2_AZM.fcs · 20220630_52_1_Processed_Concatenated_T2_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T3_AZM.fcs · 20220630_52_1_Processed_Concatenated_T3_DMSO.fcs · 20220630_52_1_Processed_Concatenated_T4_AZM.fcs · 20220630_52_1_Processed_Concatenated_T4_DMSO.fcs
· 54 20220701_54_1_Processed_Concatenated_T0_AZM.fcs · 20220701_54_1_Processed_Concatenated_T0_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T1_AZM.fcs · 20220701_54_1_Processed_Concatenated_T1_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T2_AZM.fcs · 20220701_54_1_Processed_Concatenated_T2_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T3_AZM.fcs · 20220701_54_1_Processed_Concatenated_T3_DMSO.fcs · 20220701_54_1_Processed_Concatenated_T4_AZM.fcs · 20220701_54_1_Processed_Concatenated_T4_DMSO.fcs
· 45 20220713_45_1_Processed_Concatenated_T0_AZM.fcs · 20220713_45_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T1_AZM.fcs · 20220713_45_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T2_AZM.fcs · 20220713_45_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T3_AZM.fcs · 20220713_45_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_45_1_Processed_Concatenated_T4_AZM.fcs · 20220713_45_1_Processed_Concatenated_T4_DMSO.fcs
· 55 20220713_55_1_Processed_Concatenated_T0_AZM.fcs · 20220713_55_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T1_AZM.fcs · 20220713_55_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T2_AZM.fcs · 20220713_55_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T3_AZM.fcs · 20220713_55_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_55_1_Processed_Concatenated_T4_AZM.fcs · 20220713_55_1_Processed_Concatenated_T4_DMSO.fcs
· 56 20220713_56_1_Processed_Concatenated_T0_AZM.fcs · 20220713_56_1_Processed_Concatenated_T0_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T1_AZM.fcs · 20220713_56_1_Processed_Concatenated_T1_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T2_AZM.fcs · 20220713_56_1_Processed_Concatenated_T2_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T3_AZM.fcs · 20220713_56_1_Processed_Concatenated_T3_DMSO.fcs · 20220713_56_1_Processed_Concatenated_T4_AZM.fcs · 20220713_56_1_Processed_Concatenated_T4_DMSO.fcs

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