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Cytobank specifications


Unique identifier OMICS_05619
Name Cytobank
Restrictions to use None
Maintained Yes

Publication for Cytobank

Cytobank citations


Multiplexed Quantitation of Intraphagocyte Mycobacterium tuberculosis Secreted Protein Effectors

Cell Rep
PMCID: 5946722
PMID: 29694886
DOI: 10.1016/j.celrep.2018.03.125
call_split See protocol

[…] were acquired in an LSR Fortessa flow cytometer system using BD FACSDiva software (BD Biosciences). Cytometric data were analyzed using FlowJo software (Tree Star, OR, USA) or the viSNE algorithm in Cytobank. PCA was performed by using the R function prcomp (center TRUE; scale. TRUE) on intraphagocyte secretion profiles determined for each bacterial strain as (% reporter+ T cells × MFI reporter+ […]


CD161 Defines a Functionally Distinct Subset of Pro Inflammatory Natural Killer Cells

Front Immunol
PMCID: 5900032
PMID: 29686665
DOI: 10.3389/fimmu.2018.00486

[…] in Figure S1 in Supplementary Material. Details of antibodies used are shown in Table S3 in Supplementary Material.t-Distributed stochastic neighbor embedding (t-SNE) analysis was either performed in Cytobank (; Cytobank Inc.) or in R. Biaxial gating was performed on FlowJo Version 10 software (Treestar).Fetal calf serum files were imported into R via the read.FCS function in the f […]


Analysis of cell surface and intranuclear markers on non stimulated human PBMC using mass cytometry

PLoS One
PMCID: 5864033
PMID: 29566047
DOI: 10.1371/journal.pone.0194593
call_split See protocol

[…] 4 elements EQ beads were used to normalize files using the Matlab compiler software cell normalizer. Data files were obtained in the FCS file format and analysed using FlowJo software version 10 and Cytobank cloud based platform. Beads were gated out using the following gates: 140/142Ce, 151/153Eu, 165Ho and 175/176 Lu. CD45+ events were selected for the analysis of different cell populations. Ci […]


Adaptive Reconfiguration of Natural Killer Cells in HIV 1 Infection

Front Immunol
PMCID: 5864861
PMID: 29616021
DOI: 10.3389/fimmu.2018.00474

[…] Samples were acquired on a BD Fortessa X20 using BD FACSDiva8.0 (BD Bioscience) and data analyzed using FlowJo 10 (TreeStar). Stochastic neighbor embedding (SNE) analysis was performed using the mrc.cytobank platform. The t-distributed stochastic neighbor embedding algorithm clusters cells according to expression of multiple parameters and enables visualization of high-dimensional data in two-dim […]


Sensitive and frequent identification of high avidity neo epitope specific CD8+ T cells in immunotherapy naive ovarian cancer

Nat Commun
PMCID: 5854609
PMID: 29545564
DOI: 10.1038/s41467-018-03301-0

[…] 1 in 0.1% EQ Four Element Calibration Beads solution (Fluidigm). Samples were acquired on an upgraded CyTOF using a syringe pump at 45 μL per min. FCS files were concatenated and normalized using the cytobank concatenation tool and matlab normalizer, respectively. Data were processed and analyzed with cytobank and R using the OpenCyto and cytofkit packages. […]


miR200 regulated CXCL12β promotes fibroblast heterogeneity and immunosuppression in ovarian cancers

Nat Commun
PMCID: 5849633
PMID: 29535360
DOI: 10.1038/s41467-018-03348-z

[…] the six CAF markers including CD29, FAP, SMA, FSP1, PDGFRβ, and Caveolin. Sorting of CAF subsets after surface staining was performed on FACSARIA (BD Biosciences). SPADE algorithm was performed using Cytobank (Cytobank Inc., Mountain View, CA, USA). SPADE clustering was performed using 300 nodes to generate unified trees based on the expression of the six CAF markers. CAF subset populations were m […]


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Cytobank institution(s)
Cytobank, Inc, Mountain View, CA, USA

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