Experiment Overview
| Repository ID: | FR-FCM-Z32G | Experiment name: | High dimensional immunotyping of the obese tumor microenvironment with unanchored batch correction | MIFlowCyt score: | 49.25% |
| Primary researcher: | Cara Wogsland | PI/manager: | Cara Wogsland | Uploaded by: | Cara Wogsland |
| Experiment dates: | 2017-08-09 - 2020-10-12 | Dataset uploaded: | Oct 2020 | Last updated: | Dec 2021 |
| Keywords: | [mass cytometry] [CyTOF] [Pancreatic cancer] [tumor immunology] [Breast Cancer] [Obesity] [batch correction] [mouse models] | Manuscripts: | [33653826] [PMC8033414] | ||
| Organizations: |
University of Bergen, Bergen, (Norway)
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| Purpose: | Analysis of tumor immune infiltrate in immunocompetent mice with orthotopic syngeneic tumors. This experiment contains 57 fcs files of CD45+ tumor immune infiltrate from 7 CyTOF batches across 5 tumor models in obese and non-obese settings. Files have been normalized and debarcoded. Arcsinh transformation and unanchored cydar range batch correction has been applied to channels with the "c_" prefix. Original channels are present in the files. viSNE tSNE coordinates are also present. | ||||
| Conclusion: |
Unanchored range-based batch correction using cydar in R was successful and enabled the simultaneous analysis of 7 different CyTOF batches. bioRxiv: https://doi.org/10.1101/2020.10.14.338806 |
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| Comments: |
Breast cancer models: E0771 (2 batches), Wnt1, TeLi Pancreatic cancer: C11 (2 batches), UN-KC High fat diet fed/obese mice: H Standard chow diet/non-obese mice: C Helios CyTOF, Narrow bore (HT) injector |
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| Funding: | Not disclosed | ||||
| Quality control: | Data Normalization | Normalization, Palladium barcoding, reference samples in each batch (not included here). Testing of 3 different batch correction approaches. | |||
