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downsample plugin (Becton Dickinson)

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Structured Review

Becton Dickinson downsample plugin

FItSNE projection of the various cytokine-expressing cell subtypes in PBMC and RMC. Data from healthy donor PBMC (n=8) or RMC (n=11) samples, obtained via flow cytometry, were concatenated to generate a single FItSNE projection of the different unbiased cell clusters based on their cytokine and markers expression, calculated with FlowSOM. The FItSNE projection along with the percentage of events of each cell cluster for both PBMC (A, B) and RMC (C, D) are shown. FItSNE analysis was performed with the <t>tSNE</t> function <t>in</t> <t>FlowJo,</t> FItSNE algorithm, with 3000 iterations, and a perplexity of 20.0.

Downsample Plugin, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/tsne+software/downsample+plugin/pmc10912472-88-2-4
Average 90 stars, based on 1 article reviews

downsample plugin - by Bioz Stars, 2026-09

90/100 stars

Images

1) Product Images from "Comparative analysis of human gut- and blood-derived mononuclear cells: contrasts in function and phenotype"

Article Title: Comparative analysis of human gut- and blood-derived mononuclear cells: contrasts in function and phenotype

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2024.1336480

Figure Legend Snippet: FItSNE projection of the various cytokine-expressing cell subtypes in PBMC and RMC. Data from healthy donor PBMC (n=8) or RMC (n=11) samples, obtained via flow cytometry, were concatenated to generate a single FItSNE projection of the different unbiased cell clusters based on their cytokine and markers expression, calculated with FlowSOM. The FItSNE projection along with the percentage of events of each cell cluster for both PBMC (A, B) and RMC (C, D) are shown. FItSNE analysis was performed with the tSNE function in FlowJo, FItSNE algorithm, with 3000 iterations, and a perplexity of 20.0.

Techniques Used: Expressing, Flow Cytometry

FItSNE projection of the main cell groups among the various cytokine-expressing cell subtypes in PBMC and RMC. Layers of different cell populations were removed from the original tSNE projection for better visualization of the main cell groups in PBMC (n=8) and RMC (n=11); NK and other CD3- cells (A) , CD4 + and CD8 + T cells (B) , and γδ T cells are demonstrated (C) . FItSNE analysis was performed with the tSNE function in FlowJo, FItSNE algorithm, with 3000 iterations, and a perplexity of 20.0.

Figure Legend Snippet: FItSNE projection of the main cell groups among the various cytokine-expressing cell subtypes in PBMC and RMC. Layers of different cell populations were removed from the original tSNE projection for better visualization of the main cell groups in PBMC (n=8) and RMC (n=11); NK and other CD3- cells (A) , CD4 + and CD8 + T cells (B) , and γδ T cells are demonstrated (C) . FItSNE analysis was performed with the tSNE function in FlowJo, FItSNE algorithm, with 3000 iterations, and a perplexity of 20.0.

Techniques Used: Expressing

other:

Article Title: Characterization of Natural Killer Cell Profile in a Cohort of Infected Pregnant Women and Their Babies and Its Relation to CMV Transmission
Article Snippet: The “DownSample” FlowJo plugin was run on NK cells in order to reduce and make uniform the population sizes for the further concatenation of samples from different groups into a single FCS file. tSNE was performed on the concatenated file using the “TSNE” plugin and the maps generated using data from the following compensated parameters as inputs: CD56, CD16, NKG2C, NKG2A, NKG2D, DNAM-1, CD57, KIR2DL1/S1/S3/S5, KIR2DL2/L3, and PD-1 for the phenotype analysis and CD56, CD16, NKG2C, DNAM-1, CD57, NKp46, PD-1, and CD107a for the degranulation analysis; under the following tSNE settings: iteration 1000, perplexity 30, learning rate (Eta) 910–2100, the ANNOY algorithm as the k nearest neighbors (KNN) algorithm and the fast Fourier transform (FTT) interpolation as the gradient algorithm, resulting in tSNE plots with less than 5 million events ( ).

Article Title: NK cells in peripheral blood carry trogocytosed tumor antigens from solid cancer cells
Article Snippet: To generate tSNE or UMAP embedding, a pre-gated NK cell population from each sample with the same number of cells per patient and timepoint was selected using FlowJo Downsample plugin (v3.1.0) and merged before uploading in the Cytobank cloud-based platform (Cytobank, Inc.).

Article Title: Dynamic MAIT Cell Recovery after Severe COVID-19 Is Transient with Signs of Heterogeneous Functional Anomalies.
Article Snippet: RESEARCH ARTICLE | DECEMBER 20 2023 Dynamic MAIT Cell Recovery after Severe COVID-19 Is Transient with Signs of Heterogeneous Functional Anomalies Tobias Kammann; ... et. al J Immunol ji2300639. https://doi.org/10.4049/jimmunol.2300639 D ow nloaded from http://journals.aai.org/jim m unol/article-pdf/doi/10.4049/jim m unol.2300639/1650883/ji2300639.pdf by D ELC O N - Indian Inst of Tech, G uw ahati user on 23 D ecem ber 2023

Sampling:

Article Title: A comprehensive assessment of four whole blood stabilizers for flow-cytometric analysis of leukocyte populations.
Article Snippet: .. Translational Immunology Research Program, University of Helsinki, Helsinki, Finland Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, Helsinki, Finland Division of Intensive Care Medicine, Department of Anaesthesiology, Intensive Care and Pain Medicine, University of Helsinki, Helsinki University Hospital, Helsinki, Finland Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland Meilahti Vaccine Research Center, MeVac, Infectious Diseases, Helsinki University, Helsinki University Hospital, Helsinki, Finland Division of Virology and Immunology, HUS Diagnostic Center, HUSLAB Clinical Microbiology, Helsinki, Finland Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland New Children's Hospital, Pediatric Research Center, University of Helsinki, Helsinki University Hospital, Helsinki, Finland ..

Flow Cytometry:

Image Search Results

Hypoxia promotes the development of megakaryoerythroid progenitors. (A) Schematic of myeloerythroid differentiation from hematopoietic stem cells. The surface markers used for immunophenotyping of the cells interrogated in this study are indicated. (B) Percentage of multipotent progenitors (MPP), common myeloid progenitors (CMP), megakaryoerythroid progenitors (MEP), and granulocyte−monocyte progenitors (GMP) in cultures incubated in hypoxia and normoxia. For MPPs, the percentage of positive cells in the Lin − /Live population was determined, and for CMPs, GMPs, and MEPs, the percentage of positive cells in the MPP population was determined on days 1, 7, 14, and 21. Data are represented as the mean with standard error ( n = 4). Statistical analysis was performed using the Mann-Whitney test, and p values ≤ 0.05 were considered significant. (C) tSNE analysis was performed on flow cytometry standard files. tSNE plots for day 21 analysis revealing CD34 + and CD38 + cells in normoxia and hypoxia are represented in the Lin − /Live population. (D) tSNE analysis plots revealing the distribution of CMPs, GMPs, and MEPs in the CD34 + /CD38 + population in normoxia or hypoxia on day 21 are represented. (E) Histograms for CD45Ra and CD123 expression indicating relative distribution of CMPs (CD45Ra − /CD123 lo ), GMPs (CD45Ra + /CD123 lo ), and MEPs (CD45Ra − /CD123 − ) in normoxia and hypoxia. * p < 0.05, ** p < 0.005, *** p < 0.0005.

Journal: Experimental hematology

Article Title: Hypoxia promotes erythroid differentiation through the development of progenitors and proerythroblasts

doi: 10.1016/j.exphem.2021.02.012

Figure Lengend Snippet: Hypoxia promotes the development of megakaryoerythroid progenitors. (A) Schematic of myeloerythroid differentiation from hematopoietic stem cells. The surface markers used for immunophenotyping of the cells interrogated in this study are indicated. (B) Percentage of multipotent progenitors (MPP), common myeloid progenitors (CMP), megakaryoerythroid progenitors (MEP), and granulocyte−monocyte progenitors (GMP) in cultures incubated in hypoxia and normoxia. For MPPs, the percentage of positive cells in the Lin − /Live population was determined, and for CMPs, GMPs, and MEPs, the percentage of positive cells in the MPP population was determined on days 1, 7, 14, and 21. Data are represented as the mean with standard error ( n = 4). Statistical analysis was performed using the Mann-Whitney test, and p values ≤ 0.05 were considered significant. (C) tSNE analysis was performed on flow cytometry standard files. tSNE plots for day 21 analysis revealing CD34 + and CD38 + cells in normoxia and hypoxia are represented in the Lin − /Live population. (D) tSNE analysis plots revealing the distribution of CMPs, GMPs, and MEPs in the CD34 + /CD38 + population in normoxia or hypoxia on day 21 are represented. (E) Histograms for CD45Ra and CD123 expression indicating relative distribution of CMPs (CD45Ra − /CD123 lo ), GMPs (CD45Ra + /CD123 lo ), and MEPs (CD45Ra − /CD123 − ) in normoxia and hypoxia. * p < 0.05, ** p < 0.005, *** p < 0.0005.

Article Snippet: t-Distributed stochastic neighbor embedding (tSNE) analysis was performed using FlowJo software (TreeStar) with default parameters (iterations = 1000, perplexity = 30).

Techniques: Incubation, MANN-WHITNEY, Flow Cytometry, Expressing

Hypoxia enhances expression of erythroid markers. (A) Longitudinal analysis of CD71 relative to the erythroid marker CD235a in cultures incubated in normoxia or hypoxia. Percentages of CD71 + /CD235a − , CD71 − /CD235a + , and CD71 + /CD235a + in the CD34 − /Live population are illustrated. (B) Longitudinal analysis of CD71 relative to the erythroid marker CD239 in cultures incubated in normoxia or hypoxia. Percentages of CD71 + /CD239 − , CD71 − /CD239 + , and CD71 + /CD239 + cells in the CD34 − /Live population are illustrated. Data are represented as the mean with standard error ( n = 4). Statistical analysis was performed using the Mann-Whitney test, and p values ≤ 0.05 were considered significant. (C) tSNE plots revealing distribution of CD71 + , CD235a + , and CD239 + cells on day 21 in normoxia or hypoxia. (D) tSNE plots of overlay of CD71 + , CD235a + , and CD239 + cells in normoxia or hypoxia on day 21. tSNE analysis was performed in FlowJo. * p < 0.05, ** p < 0.005, *** p < 0.0005.

Journal: Experimental hematology

Article Title: Hypoxia promotes erythroid differentiation through the development of progenitors and proerythroblasts

doi: 10.1016/j.exphem.2021.02.012

Figure Lengend Snippet: Hypoxia enhances expression of erythroid markers. (A) Longitudinal analysis of CD71 relative to the erythroid marker CD235a in cultures incubated in normoxia or hypoxia. Percentages of CD71 + /CD235a − , CD71 − /CD235a + , and CD71 + /CD235a + in the CD34 − /Live population are illustrated. (B) Longitudinal analysis of CD71 relative to the erythroid marker CD239 in cultures incubated in normoxia or hypoxia. Percentages of CD71 + /CD239 − , CD71 − /CD239 + , and CD71 + /CD239 + cells in the CD34 − /Live population are illustrated. Data are represented as the mean with standard error ( n = 4). Statistical analysis was performed using the Mann-Whitney test, and p values ≤ 0.05 were considered significant. (C) tSNE plots revealing distribution of CD71 + , CD235a + , and CD239 + cells on day 21 in normoxia or hypoxia. (D) tSNE plots of overlay of CD71 + , CD235a + , and CD239 + cells in normoxia or hypoxia on day 21. tSNE analysis was performed in FlowJo. * p < 0.05, ** p < 0.005, *** p < 0.0005.

Article Snippet: t-Distributed stochastic neighbor embedding (tSNE) analysis was performed using FlowJo software (TreeStar) with default parameters (iterations = 1000, perplexity = 30).

Techniques: Expressing, Marker, Incubation, MANN-WHITNEY

Expression of CD105 is persistent in hypoxia. (A) Longitudinal analysis of CD71 and CD105 in cultures incubated in normoxia or hypoxia. Percentages of CD71 + /CD105 − , CD71 − /CD105 + , and CD71 + /CD105 + in the CD34 − /Live population are illustrated. (B) Longitudinal analysis of CD105 relative to the erythroid marker CD235a in cultures incubated in normoxia or hypoxia. Percentages of CD105 + /CD235a − , CD105 − /CD235a + , and CD105 + /CD235s + cells in the CD34 − /Live population are illustrated. Data are represented as the mean with standard error ( n = 4). Statistical significance was calculated using the Mann-Whitney test, and p values ≤ 0.05 were considered significant. (C) tSNE plots revealing the distribution of CD105 + cells and overlay of CD71 + , CD105 + , and CD235a + cells on day 21 in normoxia or hypoxia. tSNE analysis was performed in FlowJo. (D) Longitudinal analysis of the CD49d and CD233 in cultures incubated in normoxia or hypoxia. Percentages of CD49d − /CD233 − , CD49d + /CD233 − , CD49d + /CD233 + , and CD49d + /CD233 − cells in the CD235a + population are illustrated. * p < 0.05, ** p < 0.005, *** p < 0.0005.

Journal: Experimental hematology

Article Title: Hypoxia promotes erythroid differentiation through the development of progenitors and proerythroblasts

doi: 10.1016/j.exphem.2021.02.012

Figure Lengend Snippet: Expression of CD105 is persistent in hypoxia. (A) Longitudinal analysis of CD71 and CD105 in cultures incubated in normoxia or hypoxia. Percentages of CD71 + /CD105 − , CD71 − /CD105 + , and CD71 + /CD105 + in the CD34 − /Live population are illustrated. (B) Longitudinal analysis of CD105 relative to the erythroid marker CD235a in cultures incubated in normoxia or hypoxia. Percentages of CD105 + /CD235a − , CD105 − /CD235a + , and CD105 + /CD235s + cells in the CD34 − /Live population are illustrated. Data are represented as the mean with standard error ( n = 4). Statistical significance was calculated using the Mann-Whitney test, and p values ≤ 0.05 were considered significant. (C) tSNE plots revealing the distribution of CD105 + cells and overlay of CD71 + , CD105 + , and CD235a + cells on day 21 in normoxia or hypoxia. tSNE analysis was performed in FlowJo. (D) Longitudinal analysis of the CD49d and CD233 in cultures incubated in normoxia or hypoxia. Percentages of CD49d − /CD233 − , CD49d + /CD233 − , CD49d + /CD233 + , and CD49d + /CD233 − cells in the CD235a + population are illustrated. * p < 0.05, ** p < 0.005, *** p < 0.0005.

Article Snippet: t-Distributed stochastic neighbor embedding (tSNE) analysis was performed using FlowJo software (TreeStar) with default parameters (iterations = 1000, perplexity = 30).

Techniques: Expressing, Incubation, Marker, MANN-WHITNEY

Review

downsample plugin (Becton Dickinson)

Structured Review

Images

1) Product Images from "Comparative analysis of human gut- and blood-derived mononuclear cells: contrasts in function and phenotype"

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