Experiment Overview
| Repository ID: | FR-FCM-Z36F | Experiment name: | Application of a whole blood CyTOF staining workflow to characterize COVID-19 patients | MIFlowCyt score: | 63.22% |
| Primary researcher: | Adeeb Rahman | PI/manager: | Adeeb Rahman | Uploaded by: | Adeeb Rahman |
| Experiment dates: | 2020-04-01 - 2020-12-01 | Dataset uploaded: | Dec 2020 | Last updated: | Jan 2021 |
| Keywords: | [whole blood] [mass cytometry] [CyTOF] [COVID] | Manuscripts: | [32607524] [PMC7325190] | ||
| Organizations: |
Icahn School of Medicine at Mount Sinai , New York, NY (United States of America)
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| Purpose: | We apply a streamlined CyTOF workflow to characterize whole blood samples collected longitudinally from a cohort of hospitalized COVID-19 patients and healthy controls to identify dynamic disease-associated changes in circulating immune cell frequency and phenotype. | ||||
| Conclusion: | Our data identify elevated neutrophil frequencies and reduced T cell frequencies as clear biomarkers of COVID-19 disease severity, but also highlight acute adaptive immune responses in some patients, represented by elevated frequencies of plasmablasts and activated CD4+ and CD8+ T cells. We also show profound changes in myeloid cell phenotype, including reduced HLA-DR expression and elevated CD169 expression on monocytes, and elevated CD64 expression on neutrophils. Furthermore, our longitudinal data clearly illustrate the highly dynamic nature of these phenotypic changes and establish that it is critically important to consider the time from infection onset and the kinetics of disease progression in interpreting these changes. | ||||
| Comments: | None | ||||
| Funding: | NIH U19AI118610 NIH U24AI118644 S10OD023547 | ||||
| Quality control: | Samples were stained with a lyophilized antibody panel and barcoded for sample acquisition to to reduce experimental variability. All batches were run and normalized with Fluidigm EQ normalization beads. | ||||
Experiment variables
| Conditions | |
|---|---|
| · Healthy control | 200527_PICR_MDIPAa4_PICR8026T1_debc.fcs · 200527_PICR_MDIPAa4_PICR8030T1_debc.fcs · 200529_HIMC15_MDIPAa4_PICR8016T1_debc.fcs · 200602_HIMC15_MDIPAa4_PICR8015T1_debc.fcs · 200604_HIMC15_MDIPAa4_PICR8023_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR8022_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR8024_T1_MDIPAa4_debc.fcs · 200616_MDIPAa4_PICR8025_A_debc.fcs · 200616_MDIPAa4_PICR8028_A_debc.fcs · 200616_MDIPAa4_PICR8029_A_debc.fcs · 200616_MDIPAa4_PICR8035_A_debc.fcs · 200616_MDIPAa4_PICR8104_A_debc.fcs · 200616_MDIPAa4_PICR8107_A_debc.fcs · 200616_MDIPAa4_PICR8108_A_debc.fcs · 200616_MDIPAa4_PICR8109_A_debc.fcs |
| · moderate COVID-19 | 200529_HIMC15_MDIPAa4_PICR7341T1_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7366T1_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7367T1_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7370T1_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7387_T1_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7387_T4_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7387_T8_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7392_T1_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7392_T4_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7396_T1_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7399_T1_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7399_T4_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7401_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7373_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7373_T4_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7374_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7377_T4_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7379_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7381_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7383_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7389_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7398_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7398_T4_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7398_T8_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7409_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7409_T4_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7410_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7410_T4_MDIPAa4_debc.fcs |
| · severe COVID-19 | 200527_PICR_MDIPAa4_PICR7002T1_debc.fcs · 200527_PICR_MDIPAa4_PICR7002T12_debc.fcs · 200527_PICR_MDIPAa4_PICR7002T4_debc.fcs · 200527_PICR_MDIPAa4_PICR7009T12_debc.fcs · 200527_PICR_MDIPAa4_PICR7009T4_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7354T1_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7397_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7382_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7385_T12_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7385_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7385_T4_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_A_PICR7385_T8_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7402_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7402_T4_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7402_T8_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7405_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7405_T4_MDIPAa4_debc.fcs |
| · severe COVID-19 with EOD | 200527_PICR_MDIPAa4_PICR7014T4_debc.fcs · 200527_PICR_MDIPAa4_PICR7014T8_debc.fcs · 200527_PICR_MDIPAa4_PICR7018T4_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7360T4_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7360T8_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7361T13_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7361T8_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7362T12_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7362T13_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7362T1_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7362T4_debc.fcs · 200529_HIMC15_MDIPAa4_PICR7362T8_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7356T1_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7364T1_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7368T12_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7368T13_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7368T1_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7368T4_debc.fcs · 200602_HIMC15_MDIPAa4_PICR7368T8_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7393_T1_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7393_T4_MDIPAa4_debc.fcs · 200604_HIMC15_MDIPAa4_PICR7393_T8_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7403_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7403_T4_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7403_T8_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7407_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7408_T1_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7408_T4_MDIPAa4_debc.fcs · 200604_PICR_MDIPAa4_C_PICR7408_T8_MDIPAa4_debc.fcs · 200616_MDIPAa4_PICR7363T1_debc.fcs · 200616_MDIPAa4_PICR7376T8_debc.fcs · 200616_MDIPAa4_PICR7378T1_debc.fcs · 200616_MDIPAa4_PICR7378T4_debc.fcs · 200616_MDIPAa4_PICR7378T8_debc.fcs · 200616_MDIPAa4_PICR7386T1_debc.fcs · 200616_MDIPAa4_PICR7386T4_debc.fcs |
