Web-Based Analysis and Publication of Flow Cytometry Experiments

By Nikesh Kotecha, Peter O. Krutzik, Jonathan M. Irish. Current Protocols in Cytometry, 2010

523 citations recorded by the source corpus.

Cytobank is a Web‐based application for storage, analysis, and sharing of flow cytometry experiments. Researchers use a Web browser to log in and use a wide range of tools developed for basic and advanced flow cytometry. In addition to providing access to standard cytometry tools from any computer, Cytobank creates a platform and community for developing new analysis and publication tools. Figure layouts created on Cytobank are designed to allow transparent access to the underlying experiment annotation and data processing steps. Since all flow cytometry files and analysis data are stored on a central server, experiments and figures can be viewed or edited by anyone with the proper permission, from any computer with Internet access. Once a primary researcher has performed the initial analysis of the data, collaborators can engage in experiment analysis and make their own figure layouts using the gated, compensated experiment files. Cytobank is available to the scientific community at http://www.cytobank.org. Curr. Protoc. Cytom. 53:10.17.1‐10.17.24. © 2010 by John Wiley & Sons, Inc.

Subfields: Information Systems and Management, Molecular Biology

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Citations in the corpus

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment (2020, unknown): “org was used for de-barcoding of individual samples andmanually gating of cell events to remove doublets, normalization beads and dead cells (Kotecha et al., 2010).”
Cytokine-induced memory-like natural killer cells exhibit enhanced responses against myeloid leukemia (2016, methodology): “Mass cytometry All mass cytometry data were collected on a CyTOF2 mass cytometer (Fluidigm) and analyzed using Cytobank (36).”
Mass cytometry of follicular lymphoma tumors reveals intrinsic heterogeneity in proteins including HLA-DR and a deficit in non-malignant plasmablast and germinal center B cell populations (2017, methodology): “Conflict-of-interest disclosure: J.M.I. is co-founder and board member at Cytobank Inc. and received research support from Incyte Corp. *Correspondence to: Kanutte Huse Ph.D., Oslo University Hospital, The Norwegian Radium Hospital, P.O. Box 4953 Nydalen, N-0424 Oslo, Norway, Email: Kanutte.Huse@rr-”
High‐Dimensional Single‐Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease (2018, unknown): “The appropriate transformation cofactors were determined by uploading the files into Cytobank (https://www.cytobank.org) (Kotecha et al., 2010) and using the Scales feature; thereafter transformation was carried out in MATLAB and transformed files were imported into the R environment for further pre”
FlowRepository: A resource of annotated flow cytometry datasets associated with peer‐reviewed publications (2012, methodology): “Researchers may either use the online analytical capabilities as described in Cytobank User’s Guide (5) and share dynamically created tables, illustrations, and statistics or they may upload images and relevant project ﬁles (workspaces, experiment ﬁles, etc.) from third party software tools if…”
Cytobank: providing an analytics platform for community cytometry data analysis and collaboration. (2014, methodology): “One example of making advanced computational tools accessible to biologists is the incorporation of SPADE into Cytobank (Kotecha et al. 2010), layering it with the preprocessing steps prior to advanced analysis.”
Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data (2016, methodology): “The data sets were distributed by the original authors through FlowRepository [21] and Cytobank [22].”
Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B cell Development (2014, methodology): “Mass Cytometry Analysis Processing of primary human bone marrow and mass cytometry analysis including data preprocessing is as previously described (Bendall et al., 2011; Fienberg et al., 2012; Finck et al., 2013; Kotecha et al., 2010; Amir et al., 2013).”
Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE (2011, unknown): “Data was collected using the Becton-Dickinson LSR2 flow cytometer, and transformed using inverse hyperbolic sine transformation [22].”
Primary resistance to PD-1 blockade mediated by JAK1/2 mutations (2016, methodology): “The FCS files obtained by LRSII were analyzed using the online flow cytometry program (cytobank) (37).”