Experiment Overview
| Repository ID: | FR-FCM-Z357 | Experiment name: | High-throughput flow cytometry of an AML mouse model | MIFlowCyt score: | 47.00% |
| Primary researcher: | Morteza Chalabi | PI/manager: | Morteza Chalabi | Uploaded by: | Morteza Chalabi |
| Experiment dates: | 2018-01-01 - 2021-01-01 | Dataset uploaded: | Nov 2020 | Last updated: | Jan 2021 |
| Keywords: | [high throughput flow cytometry] | Manuscripts: | |||
| Organizations: |
BRIC – University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, (Denmark)
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| Purpose: | COMPARE, an ultra-fast and robust suite for multiparametric screening, identifies phenotypic drug responses in acute myeloid leukemia | ||||
| Conclusion: | We show that COMPARE can effectively circumvent batch effects in multidimensional screening data while showing remarkably fast clustering. Using COMPARE to analyze high-throughput flow cytometry screening of AML cells, we successfully removed various biases and grouped drugs based on their responses. COMPARE effectively revealed that groups of drugs showed similar responses even though their known mechanisms are different from each other. COMPARE was sensitive enough to capture subtle changes in drug responses. We further applied COMPARE to 25 clinical flow cytometry data sets representing AML and myelodysplastic syndrome (MDS) patients. Without prior knowledge, COMPARE could effectively group the samples based on the disease with indications that the grouping also linked to clinical outcome. Thus we conclude that COMPARE is a useful tool for exploring complex multiparametric datasets and to help interpretation of drug responses. | ||||
| Comments: | AML primary splenic cells from Npm1+/cA ; Flt3+/ITD; Dnmt3a+/-; Mx1-Cre+ moribund mice were sorted for c-Kit positivity and expanded ex vivo. AML cells were treated with a library of 116 chemotherapy and immunotherapy antineoplastic agents in a five-point concentration range. Treated samples were stained with three informative cell surface antibodies and fluorescence was detected using a high-throughput flow cytometer iQue Screener Plus (Intellicyt). The uploaded fcs files are before compensation. In case of using COMPARE-suite to reproduce the result of the paper, please start from the 1st module as follows: (1) we used these channels in the 2nd and 3rd module (QC mode): VL6-H,BL1-H,BL5-H,RL1-H (2) we removed wells in the 8-9 columns of plate 1 and entire plate 3 (3) we removed BL1-H channel as of the 3rd module (correction mode) (4) we set n = 5 in the 5th module, (5) we set nn = 135 in the 8th module. | ||||
| Funding: | This work was supported through a centre grant from the Novo Nordisk Foundation (Novo Nordisk Foundation Center for Stem Cell Biology, DanStem; Grant Number NNF17CC0027852) and is also part of the Danish Research Center for Precision Medicine in Blood Cancers funded by the Danish Cancer Society (Grant number R223‐A13071) and Greater Copenhagen Health Science Partners. | ||||
| Quality control: | FCS collection for software testing | ||||
