CyTOForum

"Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating"
Peng Liu, Yuchen Pan, Hung-Ching Chang, Yusi Fang, Xiangning Xue, Jian Zou, Jessica M. Toothaker, Oluwabunmi Olaloye, Eduardo Gonzalez Santiago, Black McCourt, Vanessa Mitsialis, Pietro Presicce, Suhas G. Kallapur, Scott B. Snapper, Jia-Jun Liu, George Tseng, Liza Konnikova, Silvia Liu
bioRxiv, posted August 15, 2024
https://doi.org/10.1101/2024.08.12.607667

- will update when/if this is peer-reviewed and published

- new human PBMC and dataset new Rhesus PBMC dataset accessions not given

- reuses
Rhesus villi: 2020-Toothaker et al-Front Immunol
Human villi: 2022-Toothaker et al-Development
Human bone marrow: 2015-Levine et al-Cell
Mouse bone marrow: 2016-Samusik et al-Nat Methods

GatingMethod, tSNE, ACCENSE, CCAST, ClusterX, Cytometree, densityCUT, DensVM, DEPECHE, FLOCK, flowClust, FlowGrid, flowMeans, flowPeaks, FlowSOM, immunoClust, kmeans, PAC-MAN, Phenograph, Rclusterpp, SamSPECTRAL, SPADE, SWIFT, X-shift, DeepCyTOF, CyTOF linear classifier, ACDC, MP, OpenCyto, flowLearn

Now published:

Brief Bioinform. 2024, 26, bbae633
https://doi.org/10.1093/bib/bbae633

- "To evaluate the gating methods, we collected datasets generated by cytometry technology from both our in-house samples and publicly available sources. As shown in Table 1, six datasets were used in this study: human PBMCs, rhesus macaque PBMCs, human placental villi [27], rhesus macaque placental villi [25], human bone marrow [29], and mouse bone marrow [30]."

- "‘PBMCs’ were isolated from human blood draws via Ficoll gradient and cryopreserved as described above for the NHP blood samples. Human patients were recruited from Boston Children’s Hospital (BCH) under the BCH Institutional Review Board protocol number P00000529. They were then thawed and underwent staining for CyTOF as described below. CyTOF data for this dataset are publicly available on Cytobank (Beckman Coulter)."
- however, no Cytobank accession given

- no dataset accession given for human PBMC either