Experiment Overview
| Repository ID: | FR-FCM-Z2V9 | Experiment name: | POISED CyTOF for CyAnno | MIFlowCyt score: | 79.75% |
| Primary researcher: | abhinav Kaushik | PI/manager: | Kari Nadeau | Uploaded by: | abhinav Kaushik |
| Experiment dates: | 2017-10-24 - 2019-06-25 | Dataset uploaded: | Sep 2020 | Last updated: | Sep 2020 |
| Keywords: | [CyTOF] [CyAnno] [POISED] [peanut] | Manuscripts: | [34037686] |
|
|
| Organizations: |
Stanford University, Stanford, (USA)
|
||||
| Purpose: | We introduce CyAnno, a novel semi-automated approach for deconvoluting the unlabeled cytometry dataset based on a machine learning framework utilizing manually gated training data that allows the integrative modeling of gated cell types and the ungated cells. In order to validate the findings, model evaluation on large independent datasets belonging to untrained batches or stimulations, we generated 30 CyTOF samples from human PBMCs, from peanut-allergic individuals. These samples were run across 7 batches with a panel of 21 lineage markers and 18 functional markers and under two different stimulations, i.e. unstimulated and peanut stimulated. 21 cell types were manually gated (including closely related cell types). | ||||
| Conclusion: | Using CyAnno on several CyTOF datasets, we demonstrated that including the ungated cells can lead to a significant increase in the prediction accuracy of the gated cell types. CyAnno can be used to identify even a single cell type, including rare cells, with higher efficacy than current state-of-the-art semi-automated approaches. | ||||
| Comments: | None | ||||
| Funding: | This work was supported by the National Institute of Allergy and Infectious Diseases (NIAID) under grants 5U19 AI104209-07, R01AI140134-01 and 5U01 AI140498-03, the Sean N Parker Center for Allergy and Asthma Research at Stanford University. Also, this work was partially supported by the National Institute of Health Grant P30-CA124435, Grant P30-DK116074, and Grant UL1-TR003142. | ||||
| Quality control: | For in-house metal conjugation, purified antibodies were purchased from BD Biosciences or Biolegend. Thus, each in-house conjugated antibody per batch of conjugation was tested and titrated using unstimulated and PMA/Ionomycin-stimulated PBMCs isolated from a buffy coat sample. Metal pre-conjugated, QA/QCed, ready-to-use antibodies were purchased from Fluidigm. The whole antibody panel was tested and validated for it's function using unstimulated and PMA/Ionomycin-stimulated PBMCs isolated from a buffy coat sample. | ||||
Experiment variables
| Timepoints | |
|---|---|
| · Baseline | export_P015-000-Pea.fcs · export_P015-000-Un.fcs · export_P042-000-Pea.fcs · export_P042-000-Un.fcs · export_P052-000-Pea.fcs · export_P052-000-Un.fcs · export_P063-000-Pea.fcs · export_P063-000-Un.fcs · export_P075-000-Pea.fcs · export_P075-000-Un.fcs · export_P079-000-Pea.fcs · export_P079-000-Un.fcs · export_P085-000-Pea.fcs · export_P085-000-Un.fcs · export_P090-000-Pea.fcs · export_P090-000-Un.fcs · export_P107-000-Pea.fcs · export_P107-000-Un.fcs · export_P111-000-Pea.fcs · export_P111-000-Un.fcs · export_P112-000-Pea.fcs · export_P112-000-Un.fcs · export_P115-000-Pea.fcs · export_P115-000-Un.fcs · export_P116-000-Pea.fcs · export_P116-000-Un.fcs · export_P117-000-Pea.fcs · export_P117-000-Un.fcs · export_P120-000-Pea.fcs · export_P120-000-Un.fcs |
| Conditions | |
|---|---|
| · Peanut Stimulated | export_P015-000-Pea.fcs · export_P042-000-Pea.fcs · export_P052-000-Pea.fcs · export_P063-000-Pea.fcs · export_P075-000-Pea.fcs · export_P079-000-Pea.fcs · export_P085-000-Pea.fcs · export_P090-000-Pea.fcs · export_P107-000-Pea.fcs · export_P111-000-Pea.fcs · export_P112-000-Pea.fcs · export_P115-000-Pea.fcs · export_P116-000-Pea.fcs · export_P117-000-Pea.fcs · export_P120-000-Pea.fcs |
| · Unstimulated | export_P015-000-Un.fcs · export_P042-000-Un.fcs · export_P052-000-Un.fcs · export_P063-000-Un.fcs · export_P075-000-Un.fcs · export_P079-000-Un.fcs · export_P085-000-Un.fcs · export_P090-000-Un.fcs · export_P107-000-Un.fcs · export_P111-000-Un.fcs · export_P112-000-Un.fcs · export_P115-000-Un.fcs · export_P116-000-Un.fcs · export_P117-000-Un.fcs · export_P120-000-Un.fcs |
