Experiment Overview
| Repository ID: | FR-FCM-Z7E5 | Experiment name: | Phenotypic profiling of HIV-responsive NK cells with mass cytometry | MIFlowCyt score: | 83.00% |
| Primary researcher: | Ruoxi Pi | PI/manager: | Catherine Blish | Uploaded by: | Ruoxi Pi |
| Experiment dates: | 2018-01-21 - 2018-03-03 | Dataset uploaded: | Apr 2024 | Last updated: | Oct 2025 |
| Keywords: | [CyTOF] [natural killer (NK) cells] [human immunodeficiency virus (HIV)] | Manuscripts: | |||
| Organizations: |
Stanford University, Department of Medicine, Division of Infectious Diseases, Palo Alto, California (USA)
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| Purpose: | The purpose of this experiment is to profile the phenotype of the NK cells that are responsive to autologous HIV-infected CD4+ T cells. In this experiment, NK cells were co-cultured with autologous HIV-infected and mock-infected CD4+ T cells. The expression of NK cell surface receptors and functional markers were profiled with CyTOF analysis. By comparing the expression of NK cell surface receptors in the NK cells that are functional (expressing any of the functional markers CD107a, IFNgamma and TNFalpha) and not functional of responding to HIV-infected cells, we identified the NK cell receptors that are more predictive of the functional NK cells and evaluated if they are specific to HIV by comparing to the predictors of the functional NK cells when co-cultured with mock-infected CD4+ T cells. | ||||
| Conclusion: | We identified multiple NK cell receptors to be predictive of functional responding NK cells and multiple NK cells receptors to be predictive of non-functional NK cells when NK cells were co-cultured with autologous HIV-infected CD4+ T cells. The top three predictors of functional responding NK cells are TIGIT, NKp30 and KIR3DL1, and the top three predictors of non-functional NK cells are CD16, NKp46, and CD62L. When the same analysis was performed on NK cells co-cultured with mock-infected CD4+ T cells, we found that many of the predictors of functional responding NK cells are similar, suggesting that the responding NK cell phenotype identified was not unique to HIV infection. | ||||
| Comments: | The fcs files uploaded here are raw fcs files that have been normalized with EQ Beads. The fcs files were analyzed to gate on CD107a+, IFNgamma+ and TNFalpha+ cells within the NK cell population. Functional NK cells were identified with Boolean OR gate to include the cells that are stained positive for any of CD107a, IFNgamma, and TNFalpha. Non-functional NK cells were identified to be negative for all of CD107a, IFNgamma, and TNFalpha. Phenotypic analysis was performed on functional and non-functional NK cells. | ||||
| Funding: | This work was supported by the National Institutes of Health (NIH DP1 DA046089, C.A.B). | ||||
| Quality control: | None | ||||
Experiment variables
| Conditions | |
|---|---|
| · NK cells were co-cultured with autologous HIV-infected CD4+ T cells | NZ03 NK + Q23 CD4 _01_normalized.fcs · NZ04 NK + Q23 CD4_02_normalized.fcs · NZ05 NK + Q23 CD4_00_normalized.fcs · NZ07 Q23 CD4 + NK_00_normalized.fcs · NZ08 Q23 CD4 + NK_00_normalized.fcs · NZ11 Q23 CD4 + NK_00_normalized.fcs · NZ12 Q23 CD4 + NK_00_normalized.fcs · NZ13 NK + Q23 CD4_00_normalized.fcs · NZ14 NK + Q23 CD4_01_normalized.fcs · NZ15 NK + Q23 CD4_00_normalized.fcs · NZ16 NK + Q23 CD4_01_normalized.fcs · NZ17 NK + Q23 CD4_02_normalized.fcs · NZ18 NK + Q23 CD4_00_normalized.fcs · NZ19 NK + Q23 CD4_01_normalized.fcs · NZ20 NK + Q23 CD4_00_normalized.fcs · NZ21 NK + Q23 CD4_00_normalized.fcs · NZ23 NK + Q23 CD4_04_normalized.fcs · NZ25 NK + Q23 CD4_04_normalized.fcs · NZ26 NK + Q23 CD4_concat_1_normalized.fcs · NZ27 NK + Q23 CD4_02_normalized.fcs |
| · NK cells were co-cultured with autologous mock-infected CD4+ T cells | NZ03 NK + UI CD4 _01_normalized.fcs · NZ04 NK + UI CD4_02_normalized.fcs · NZ05 NK + UI CD4_00_normalized.fcs · NZ07 UI CD4 + NK_00_normalized.fcs · NZ08 UI CD4 + NK_00_normalized.fcs · NZ11 UI CD4 + NK_00_normalized.fcs · NZ12 UI CD4 + NK_00_normalized.fcs · NZ13 NK + UI CD4_00_normalized.fcs · NZ14 NK + UI CD4_01_normalized.fcs · NZ15 NK + UI CD4_00_normalized.fcs · NZ16 NK + UI CD4_concat_1_normalized.fcs · NZ17 NK + UI CD4_02_normalized.fcs · NZ18 NK + UI CD4_00_normalized.fcs · NZ19 NK + UI CD4_01_normalized.fcs · NZ20 NK + UI CD4_00_normalized.fcs · NZ21 NK + UI CD4_00_normalized.fcs · NZ23 NK + UI CD4_03_normalized.fcs · NZ25 NK + UI CD4_03_normalized.fcs · NZ26 NK + UI CD4_05_normalized.fcs · NZ27 NK + UI CD4_01_normalized.fcs |
| Individuals | |
|---|---|
| · Donor NZ03 | NZ03 NK + Q23 CD4 _01_normalized.fcs · NZ03 NK + UI CD4 _01_normalized.fcs |
| · Donor NZ04 | NZ04 NK + Q23 CD4_02_normalized.fcs · NZ04 NK + UI CD4_02_normalized.fcs |
| · Donor NZ05 | NZ05 NK + Q23 CD4_00_normalized.fcs · NZ05 NK + UI CD4_00_normalized.fcs |
| · Donor NZ07 | NZ07 Q23 CD4 + NK_00_normalized.fcs · NZ07 UI CD4 + NK_00_normalized.fcs |
| · Donor NZ08 | NZ08 Q23 CD4 + NK_00_normalized.fcs · NZ08 UI CD4 + NK_00_normalized.fcs |
| · Donor NZ11 | NZ11 Q23 CD4 + NK_00_normalized.fcs · NZ11 UI CD4 + NK_00_normalized.fcs |
| · Donor NZ12 | NZ12 Q23 CD4 + NK_00_normalized.fcs · NZ12 UI CD4 + NK_00_normalized.fcs |
| · Donor NZ13 | NZ13 NK + Q23 CD4_00_normalized.fcs · NZ13 NK + UI CD4_00_normalized.fcs |
| · Donor NZ14 | NZ14 NK + Q23 CD4_01_normalized.fcs · NZ14 NK + UI CD4_01_normalized.fcs |
| · Donor NZ15 | NZ15 NK + Q23 CD4_00_normalized.fcs · NZ15 NK + UI CD4_00_normalized.fcs |
| · Donor NZ16 | NZ16 NK + Q23 CD4_01_normalized.fcs · NZ16 NK + UI CD4_concat_1_normalized.fcs |
| · Donor NZ17 | NZ17 NK + Q23 CD4_02_normalized.fcs · NZ17 NK + UI CD4_02_normalized.fcs |
| · Donor NZ18 | NZ18 NK + Q23 CD4_00_normalized.fcs · NZ18 NK + UI CD4_00_normalized.fcs |
| · Donor NZ19 | NZ19 NK + Q23 CD4_01_normalized.fcs · NZ19 NK + UI CD4_01_normalized.fcs |
| · Donor NZ20 | NZ20 NK + Q23 CD4_00_normalized.fcs · NZ20 NK + UI CD4_00_normalized.fcs |
| · DOnor NZ21 | NZ21 NK + Q23 CD4_00_normalized.fcs · NZ21 NK + UI CD4_00_normalized.fcs |
| · Donor NZ23 | NZ23 NK + Q23 CD4_04_normalized.fcs · NZ23 NK + UI CD4_03_normalized.fcs |
| · Donor NZ25 | NZ25 NK + Q23 CD4_04_normalized.fcs · NZ25 NK + UI CD4_03_normalized.fcs |
| · Donor NZ26 | NZ26 NK + Q23 CD4_concat_1_normalized.fcs · NZ26 NK + UI CD4_05_normalized.fcs |
| · Donor NZ27 | NZ27 NK + Q23 CD4_02_normalized.fcs · NZ27 NK + UI CD4_01_normalized.fcs |
