Experiment Overview
| Repository ID: | FR-FCM-Z29N | Experiment name: | Large Scale HLA Tetramer Tracking of T Cells Throughout Dengue Infection Using Mass Cytometry | MIFlowCyt score: | 68.50% |
| Primary researcher: | Melissa Chng | PI/manager: | Melissa Chng | Uploaded by: | Melissa Chng |
| Experiment dates: | 2016-10-29 - | Dataset uploaded: | Sep 2019 | Last updated: | Nov 2021 |
| Keywords: | [T cell] [memory] [mass cytometry] [CyTOF] [Dengue] [DENV] [CD57] [IL-7R] [CD127] [tetramer] | Manuscripts: | [31757672] | ||
| Organizations: |
Agency for Science, Technology and Research, Singapore Immunology Network, Singapore, (Singapore)
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| Purpose: | T cells play important multi-faceted roles during dengue infection and understanding their responses is important for defining correlates of protective immunity and identifying effective vaccine antigens. Using mass cytometry and a highly-multiplexed peptide-human leukocyte antigen (HLA) tetramer staining strategy, we probed T cells from dengue patients for a total of 430 dengue and control candidate epitopes together with key markers of activation, trafficking, and differentiation. | ||||
| Conclusion: | During acute disease, dengue-specific CD8+ T cells expressed a distinct profile of activation and trafficking receptors that distinguished them from non-dengue-specific T cells. During convalescence, dengue-specific T cells differentiated into two major cell fates, CD57+ CD127- terminally differentiated senescent memory cells and CD127+ CD57- proliferation-capable memory cells. | ||||
| Comments: | Preprocessing: After mass cytometry acquisition, the signal of each parameter was normalized based on the equilibration beads added to each sample (Finck et al., 2013). All zero values were randomized by an R-script that uniformly distributes values between minus-one and zero. Individual samples were debarcoded manually in FlowJo v10 (Treestar, Inc.). Gated for DNA_1 and DNA_2 double positive, Cisplatin-negative, CD14-negative, CD45-positive cells. Experiments 1 and 2 have a different staining panel than Experiment 3. Experiments 1 and 2 were acquired on the CyTOF 2 while Experiment 3 was acquired on the Helios. | ||||
| Funding: | This work was supported by the SIgN immune monitoring platform (E.W.N.), SIgN core funding (E.W.N.), Singapore NMRC New Investigator grant (L.R.) and by a NMRC Open Fund – Individual Research Grant (L.R.). | ||||
| Quality control: | The same control sample FMFG was used in all experiments. | ||||
Experiment variables
| Timepoints | |
|---|---|
| · V1 | CD45 Broad_1_01_Mab 69_V1.fcs · CD45 Broad_1_04_Mab 139_V1.fcs · CD45 Broad_1_08_Mab 141_V1.fcs · CD45 Broad_1_11_Mab 144_V1.fcs · CD45 Broad_2_01_Mab 119_V1.fcs · CD45 Broad_2_04_Mab 169_V1.fcs · CD45 Broad_2_08_Mab 140_V1.fcs · CD45 Broad_2_11_Mab 71_V1.fcs · CD45 Broad_3_01_Mab 58_V1.fcs · CD45 Broad_3_04_Mab 101_V1.fcs · CD45 Broad_3_07_Mab 133_V1.fcs · CD45 Broad_3_10_Mab 142_V1.fcs · CD45 Broad_3_13_Mab 143_V1.fcs · CD45 Broad_3_16_Mab 154_V1.fcs |
| · V2 | CD45 Broad_1_02_Mab 69_V2.fcs · CD45 Broad_1_05_Mab 139_V2.fcs · CD45 Broad_1_09_Mab 141_V2.fcs · CD45 Broad_1_12_Mab 144_V2.fcs · CD45 Broad_2_02_Mab 119_V2.fcs · CD45 Broad_2_05_Mab 136_V2.fcs · CD45 Broad_2_09_Mab 140_V2.fcs · CD45 Broad_2_12_Mab 71_V2.fcs · CD45 Broad_3_02_Mab 58_V2.fcs · CD45 Broad_3_05_Mab 101_V2.fcs · CD45 Broad_3_08_Mab 133_V2.fcs · CD45 Broad_3_11_Mab 142_V2.fcs · CD45 Broad_3_14_Mab 143_V2.fcs · CD45 Broad_3_17_Mab 154_V2.fcs |
| · V3 | CD45 Broad_1_03_Mab 69_V3.fcs · CD45 Broad_1_06_Mab 139_V3.fcs · CD45 Broad_1_10_Mab 141_V3.fcs · CD45 Broad_1_13_Mab 144_V3.fcs · CD45 Broad_2_03_Mab 119_V3.fcs · CD45 Broad_2_06_Mab 136_V3.fcs · CD45 Broad_2_10_Mab 140_V3.fcs · CD45 Broad_2_13_Mab 160_V3.fcs · CD45 Broad_3_03_Mab 58_V3.fcs · CD45 Broad_3_06_Mab 101_V3.fcs · CD45 Broad_3_09_Mab 133_V3.fcs · CD45 Broad_3_12_Mab 142_V3.fcs · CD45 Broad_3_15_Mab 143_V3.fcs |
| Conditions | |
|---|---|
| · Dengue | CD45 Broad_1_01_Mab 69_V1.fcs · CD45 Broad_1_02_Mab 69_V2.fcs · CD45 Broad_1_03_Mab 69_V3.fcs · CD45 Broad_1_04_Mab 139_V1.fcs · CD45 Broad_1_05_Mab 139_V2.fcs · CD45 Broad_1_06_Mab 139_V3.fcs · CD45 Broad_1_08_Mab 141_V1.fcs · CD45 Broad_1_09_Mab 141_V2.fcs · CD45 Broad_1_10_Mab 141_V3.fcs · CD45 Broad_1_11_Mab 144_V1.fcs · CD45 Broad_1_12_Mab 144_V2.fcs · CD45 Broad_1_13_Mab 144_V3.fcs · CD45 Broad_2_01_Mab 119_V1.fcs · CD45 Broad_2_02_Mab 119_V2.fcs · CD45 Broad_2_03_Mab 119_V3.fcs · CD45 Broad_2_04_Mab 169_V1.fcs · CD45 Broad_2_05_Mab 136_V2.fcs · CD45 Broad_2_06_Mab 136_V3.fcs · CD45 Broad_2_08_Mab 140_V1.fcs · CD45 Broad_2_09_Mab 140_V2.fcs · CD45 Broad_2_10_Mab 140_V3.fcs · CD45 Broad_2_11_Mab 71_V1.fcs · CD45 Broad_2_12_Mab 71_V2.fcs · CD45 Broad_2_13_Mab 160_V3.fcs · CD45 Broad_3_01_Mab 58_V1.fcs · CD45 Broad_3_02_Mab 58_V2.fcs · CD45 Broad_3_03_Mab 58_V3.fcs · CD45 Broad_3_04_Mab 101_V1.fcs · CD45 Broad_3_05_Mab 101_V2.fcs · CD45 Broad_3_06_Mab 101_V3.fcs · CD45 Broad_3_07_Mab 133_V1.fcs · CD45 Broad_3_08_Mab 133_V2.fcs · CD45 Broad_3_09_Mab 133_V3.fcs · CD45 Broad_3_10_Mab 142_V1.fcs · CD45 Broad_3_11_Mab 142_V2.fcs · CD45 Broad_3_12_Mab 142_V3.fcs · CD45 Broad_3_13_Mab 143_V1.fcs · CD45 Broad_3_14_Mab 143_V2.fcs · CD45 Broad_3_15_Mab 143_V3.fcs · CD45 Broad_3_16_Mab 154_V1.fcs · CD45 Broad_3_17_Mab 154_V2.fcs |
| · Healthy | CD45 Broad_1_07_FMFG_V0.fcs · CD45 Broad_1_14_AV69_V0.fcs · CD45 Broad_2_07_FMFG_V0.fcs · CD45 Broad_2_14_2EUG_V0.fcs · CD45 Broad_3_18_AUX6_V0.fcs · CD45 Broad_3_19_FMFG_V0.fcs · CD45 Broad_3_20_2EUG_V0.fcs |
| Individuals | |
|---|---|
| · Mab 69 | CD45 Broad_1_01_Mab 69_V1.fcs · CD45 Broad_1_02_Mab 69_V2.fcs · CD45 Broad_1_03_Mab 69_V3.fcs |
| · Mab 139 | CD45 Broad_1_04_Mab 139_V1.fcs · CD45 Broad_1_05_Mab 139_V2.fcs · CD45 Broad_1_06_Mab 139_V3.fcs |
| · Mab 141 | CD45 Broad_1_08_Mab 141_V1.fcs · CD45 Broad_1_09_Mab 141_V2.fcs · CD45 Broad_1_10_Mab 141_V3.fcs |
| · Mab 144 | CD45 Broad_1_11_Mab 144_V1.fcs · CD45 Broad_1_12_Mab 144_V2.fcs · CD45 Broad_1_13_Mab 144_V3.fcs |
| · Mab 119 | CD45 Broad_2_01_Mab 119_V1.fcs · CD45 Broad_2_02_Mab 119_V2.fcs · CD45 Broad_2_03_Mab 119_V3.fcs |
| · Mab 169 | CD45 Broad_2_04_Mab 169_V1.fcs |
| · Mab 136 | CD45 Broad_2_05_Mab 136_V2.fcs · CD45 Broad_2_06_Mab 136_V3.fcs |
| · Mab 140 | CD45 Broad_2_08_Mab 140_V1.fcs · CD45 Broad_2_09_Mab 140_V2.fcs · CD45 Broad_2_10_Mab 140_V3.fcs |
| · Mab 71 | CD45 Broad_2_11_Mab 71_V1.fcs · CD45 Broad_2_12_Mab 71_V2.fcs |
| · Mab 160 | CD45 Broad_2_13_Mab 160_V3.fcs |
| · Mab 58 | CD45 Broad_3_01_Mab 58_V1.fcs · CD45 Broad_3_02_Mab 58_V2.fcs · CD45 Broad_3_03_Mab 58_V3.fcs |
| · Mab 101 | CD45 Broad_3_04_Mab 101_V1.fcs · CD45 Broad_3_05_Mab 101_V2.fcs · CD45 Broad_3_06_Mab 101_V3.fcs |
| · Mab 133 | CD45 Broad_3_07_Mab 133_V1.fcs · CD45 Broad_3_08_Mab 133_V2.fcs · CD45 Broad_3_09_Mab 133_V3.fcs |
| · Mab 142 | CD45 Broad_3_10_Mab 142_V1.fcs · CD45 Broad_3_11_Mab 142_V2.fcs · CD45 Broad_3_12_Mab 142_V3.fcs |
| · Mab 143 | CD45 Broad_3_13_Mab 143_V1.fcs · CD45 Broad_3_14_Mab 143_V2.fcs · CD45 Broad_3_15_Mab 143_V3.fcs |
| · Mab 154 | CD45 Broad_3_16_Mab 154_V1.fcs · CD45 Broad_3_17_Mab 154_V2.fcs |
