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)
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| 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 |
