Journal: Frontiers in Immunology

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

doi: 10.3389/fimmu.2024.1336480

Figure Lengend 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.

Article Snippet: For the tSNE analysis, FlowJo Downsample plugin was used to ensure similar number of events in all samples.

Techniques: Expressing, Flow Cytometry

Journal: Frontiers in Immunology

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

doi: 10.3389/fimmu.2024.1336480

Figure Lengend 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.

Article Snippet: For the tSNE analysis, FlowJo Downsample plugin was used to ensure similar number of events in all samples.

Techniques: Expressing

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

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

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