Experiment Overview
| Repository ID: | FR-FCM-Z74D | Experiment name: | Human multi-tissue deceased organ donor immune cell dataset | MIFlowCyt score: | 79.09% |
| Primary researcher: | Valerie Coppard | PI/manager: | Joanne Jones | Uploaded by: | Zoya Georgieva |
| Experiment dates: | 2019-10-01 - 2023-07-16 | Dataset uploaded: | Dec 2023 | Last updated: | Dec 2023 |
| Keywords: | [high-dimenisional flow cytometry] [dimensionality reduction] [FlowAtlas] [EmbedSOM clustering] | Manuscripts: | |||
| Organizations: |
University of Cambridge, Clinical Neurosciences, Cambridge, (UK)
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| Purpose: | Characterisation of human tissue-resident T and Treg cell subsets. This dataset was used for the development of an interactive web-based high-dimensional data analysis tool called FlowAtlas. FlowAtlas works in tandem with FlowJo and enables fast and intuitive analysis of high-dimensional flow cytometry data including dimensionality reduction without down-sampling. It allows exploration of cluster characteristics, and integration of non-identical data-sets to enable data re-use and validation. | ||||
| Conclusion: | T-reg cells found in human tissues are a heterogeneous population expressing different chemokine receptors, as well as tissue residency markers such as CD69. We explored Treg heterogeneity by performing dimensionality reduction, clustering and population annotation in FlowAtlas. FlowAtlas workflow successfully integrated immune cells stained with 3 different panels, from multiple tissues derived from 5 separate donors. FlowAtlas was relatively robust to small to moderate differences in panel design (tissues were stained with 3 different panels; we only exported and analysed T-cells). This property of FlowAtlas is also demonstrated on healthy control blood from 2 healthy donors, which we stained with the 3 non-identical panels. | ||||
| Comments: | Instructions on downloading and using FlowAtlas can be found here: https://github.com/gszep/FlowAtlas.jl These FCS files only show single live T-cell events, and only parameters shared between all donors. Gating hierarchy, FlowJo workspace and FlowAtlas SOM are provided. | ||||
| Funding: | Not disclosed | ||||
| Quality control: | Human tissue-derived immune dataset was stained with lot-specific antibody sets under identical conditions. Cytometer QC was performed (using CS&T, and 8-peak beads) before each data acquisition. | ||||
Experiment variables
| Individuals | |
|---|---|
| · Donor 390C | exp_390C_BM_027_T cells.fcs · exp_390C_Ileum_028_T cells.fcs · exp_390C_Liver_026_T cells.fcs · exp_390C_Lung_029_T cells.fcs · exp_390C_Mes LN_024_T cells.fcs · exp_390C_Spleen_025_T cells.fcs · exp_390C_Thor LN_023_T cells.fcs |
| · Donor 403C | exp_403C_donor_BM_024_T cells.fcs · exp_403C_donor_Liver_025_T cells.fcs · exp_403C_donor_Lung_026_T cells.fcs · exp_403C_donor_Spleen_022_T cells.fcs · exp_403C_donor_mLN_027_T cells.fcs · exp_403C_donor_tLN_028_T cells.fcs · exp_423_Donor_thLN_030_T cells.fcs |
| · Donor 412C | exp_Specimen_001_412C Ileum_027_T cells.fcs · exp_Specimen_001_412C Liver_033_T cells.fcs · exp_Specimen_001_412C Pre Ed Blood_025_T cells.fcs · exp_Specimen_001_412C Spleen_029_T cells.fcs · exp_Specimen_001_412C mLN_026_T cells.fcs · exp_Specimen_001_412C tLN_034_T cells.fcs |
| · Donor 423C | exp_423_Donor_BM_028_T cells.fcs · exp_423_Donor_Ileum_033_T cells.fcs · exp_423_Donor_Liver_022_T cells.fcs · exp_423_Donor_Lung_032_T cells.fcs · exp_423_Donor_Pre-blood_023_T cells.fcs · exp_423_Donor_Spleen_026_T cells.fcs · exp_423_Donor_mLN_029_T cells.fcs |
| · Donor 428C | exp_428_Donor_BM_026_T cells.fcs · exp_428_Donor_Ileum_030_T cells.fcs · exp_428_Donor_Lung_029_T cells.fcs · exp_428_Donor_Spleen_024_T cells.fcs · exp_428_Donor_thLN_027_T cells.fcs |
| · Healthy control blood donor A | exp_exp_Donor__A_panel-A_Clean cells_T cells.fcs · exp_exp_Donor__A_panel-B_Clean cells_T cells.fcs · exp_exp_Donor__A_panel-C_Clean cells_T cells.fcs |
| · Healthy control blood donor B | exp_exp_Donor__B_panel-A_Clean cells_T cells.fcs · exp_exp_Donor__B_panel-B_Clean cells_T cells.fcs · exp_exp_Donor__B_panel-C_Clean cells_T cells.fcs |
| Conditions | |
|---|---|
| · Spleen | exp_390C_Spleen_025_T cells.fcs · exp_403C_donor_Spleen_022_T cells.fcs · exp_423_Donor_Spleen_026_T cells.fcs · exp_428_Donor_Spleen_024_T cells.fcs · exp_Specimen_001_412C Spleen_029_T cells.fcs |
| · Bone marrow | exp_390C_BM_027_T cells.fcs · exp_403C_donor_BM_024_T cells.fcs · exp_423_Donor_BM_028_T cells.fcs · exp_428_Donor_BM_026_T cells.fcs |
| · Liver | exp_390C_Liver_026_T cells.fcs · exp_403C_donor_Liver_025_T cells.fcs · exp_423_Donor_Liver_022_T cells.fcs · exp_Specimen_001_412C Liver_033_T cells.fcs |
| · thoracic lymph nodes | exp_390C_Thor LN_023_T cells.fcs · exp_403C_donor_tLN_028_T cells.fcs · exp_423_Donor_thLN_030_T cells.fcs · exp_428_Donor_thLN_027_T cells.fcs · exp_Specimen_001_412C tLN_034_T cells.fcs |
| · mesenteric lymph nodes | exp_390C_Mes LN_024_T cells.fcs · exp_403C_donor_mLN_027_T cells.fcs · exp_423_Donor_mLN_029_T cells.fcs · exp_Specimen_001_412C mLN_026_T cells.fcs |
| · Lung | exp_390C_Lung_029_T cells.fcs · exp_403C_donor_Lung_026_T cells.fcs · exp_423_Donor_Lung_032_T cells.fcs · exp_428_Donor_Lung_029_T cells.fcs |
| · Ileum | exp_390C_Ileum_028_T cells.fcs · exp_423_Donor_Ileum_033_T cells.fcs · exp_428_Donor_Ileum_030_T cells.fcs · exp_Specimen_001_412C Ileum_027_T cells.fcs |
| · Deceased donor blood | exp_423_Donor_Pre-blood_023_T cells.fcs · exp_Specimen_001_412C Pre Ed Blood_025_T cells.fcs |
| · Healthy (live) donor blood | exp_exp_Donor__A_panel-A_Clean cells_T cells.fcs · exp_exp_Donor__A_panel-B_Clean cells_T cells.fcs · exp_exp_Donor__A_panel-C_Clean cells_T cells.fcs · exp_exp_Donor__B_panel-A_Clean cells_T cells.fcs · exp_exp_Donor__B_panel-B_Clean cells_T cells.fcs · exp_exp_Donor__B_panel-C_Clean cells_T cells.fcs |
