2-way analysis of variance (anova) and holm-sidak multiple comparisons tests  (GraphPad Software Inc)

Journal: Translational Vision Science & Technology

Article Title: Treatment Efficacy of a Dual Release of Aflibercept and Dexamethasone From a Single Hydrogel Drug Delivery System in a Rodent Model

doi: 10.1167/tvst.14.6.31

Figure Lengend Snippet: Percent changes in CNV lesion area relative to week 0 for all treatment groups at each time point. Experiment groups included: No Treatment ( black ; n = 30 lesions), Blank-DDS ( blue ; n = 28 lesions), Bolus AFL ( pink ; n = 36 lesions), AFL-DDS ( green ; n = 35 lesions), DEX-DDS ( dark purple ; n = 35 lesions), and Combo-DDS ( light purple ; n = 32 lesions). Statistically significant differences were determined between groups using Holm-Sidak multiple comparisons tests after repeated-measures 2-way ANOVA. Statistical differences of P < 0.05 is represented by *, P < 0.01 is represented by **, P < 0.001 is represented by ***, and P < 0.0001 by ****.

Article Snippet: Statistical analysis will be performed with 2-way analysis of variance (ANOVA) and Holm-Sidak multiple comparisons tests (GraphPad Prism 9).

Techniques:

Journal: Translational Vision Science & Technology

Article Title: Treatment Efficacy of a Dual Release of Aflibercept and Dexamethasone From a Single Hydrogel Drug Delivery System in a Rodent Model

doi: 10.1167/tvst.14.6.31

Figure Lengend Snippet: Histological evaluation of CNV lesions. ( a ) Representative histology images of CNV lesions from the No Treatment group ( black ), the Blank-DDS group ( blue ), the Bolus AFL group ( pink ), the AFL-DDS group ( green ), the DEX-DDS group ( dark purple ), and the Combo-DDS group ( light purple ). ( b ) Representative images for No Treatment. ( c ) Representative image for Combo-DDS. Statistically significant differences between groups were determined using Holm-Sidak multiple comparisons tests after repeated-measures 1-way ANOVA. Statistical differences of P <0.05 is represented by *.

Article Snippet: Statistical analysis will be performed with 2-way analysis of variance (ANOVA) and Holm-Sidak multiple comparisons tests (GraphPad Prism 9).

Techniques:

Journal: bioRxiv

Article Title: Actionable biological programs to enhance EGFR-targeted therapy response unveiled by single-cell lineage tracing in clinically relevant lung cancer models

doi: 10.1101/2025.05.19.654081

Figure Lengend Snippet: (a) Time points of single-cell suspension collection from barcoded TH107 PDOs upon EGFR targeted therapy using osimertinib. (b, c) Assessment of osimertinib sensitivity by 3D-CTG (b) and high-magnification images (c) of TH107 PDOs at D0-D30 upon osimertinib or DMSO treatments (Parental: treatment-naive TH107 PDOs; Persisters: osimertinib persisters TH107 PDOs; p-value calculated using Two-way ANOVA with Sidak’s multiple comparison test). (d) Identification of four distinct lineage populations (L.A, L.B, L.C, L.D) differentially enriched at D7 and D14 in osimertinib-treated TH107 PDOs normalized to DMSO control. (e) Genomic barcode frequency scores for L.A-L.D populations highlight a gradual enrichment at D14 of the L.D population upon osimertinib treatment (p-values calculated using the Mann-Whitney-Wilcoxon test). (f) Lineage population abundances over the entire time course of the experiment show the distinctiveness behavior of the four lineage populations among osimertinb and DMSO-treated TH107 PDOs. (g) Pathway analysis of gene expression (iPAGE) comparing L.D population versus rest (L.A-L.C) at D0. All individual sequenced genes are sorted by log2FC and divided into 9 equally populated bins from lowest (negative) log2FC (left) to greatest log2FC (right). The red bar within the black header indicates the range of log2FC values in each bin. The heatmap is colored by the enrichment or depletion of the gene in each bin. The top/right-most iPAGE bin, containing genes with the greatest log2FC values, is significantly enriched for genes in the Hallmark Hedgehog Signaling gene set. The significance of the mutual information value (bits) is calculated using a non-parametric randomization test (see Methods). (h) Dotplot of Hallmark Hedgehog Signaling Gene Set genes present in the top iPAGE bin. See also Supplementary Figures 1, and 2.

Article Snippet: Statistical significance for the functional tests was calculated using Two-way ANOVA with Sidak’s multiple comparison test, one-way ANOVA with Tukey’s multiple comparison test, or Student T-test (GraphPad Prism vs 10.3.0).

Techniques: Suspension, Comparison, Control, MANN-WHITNEY, Gene Expression

Journal: bioRxiv

Article Title: Actionable biological programs to enhance EGFR-targeted therapy response unveiled by single-cell lineage tracing in clinically relevant lung cancer models

doi: 10.1101/2025.05.19.654081

Figure Lengend Snippet: (a, b) Functional crystal violet assay quantification in 2D- (a) and 3D soft agar colony formation (b) cultures with lineage A enriched (L.A) or unsorted control (U.C.) H1975 cells; quantification of the crystal violet OD (a) or the number of 3D colonies (b) is provided (n = 2-3 replicates per experimental group; p-value calculated using Student’s t-test). (c) Functional in vivo experiments with lineage A enriched (L.A) or unsorted control (U.C.) H1975 CDXs treated with osimertinib or vehicle control (p-value calculated using One-way ANOVA with Tukey’s multiple comparison test). (d, e) The tumor volume fold change was calculated from each xenograft (d) and response to osimertinib classified with RECIST criteria (e) (p-value calculated using Two-way ANOVA with Sidak’s multiple comparison test). (f, g) Functional tests using CRISPR-Cas9 lentiviral infection with sgRNA targeting FOXD1 protein and 3D-soft agar colony formation assay using unsorted control (U.C.) (f) or lineage A enriched (L.A) (g) H1975 cells treated with a dose escalation of osimertinib (Osi., 2.5-10 nM). Colonies were stained with crystal violet at day 21 and quantified (f, g) (n = 3 replicates per experimental group; p-value calculated using Two-way ANOVA with Sidak’s multiple comparison test). (Osi.: osimertinib; CR: complete response; PR: partial response; SD: stable disease; PD: progressive disease). See also Supplementary Figures 6 and 7.

Article Snippet: Statistical significance for the functional tests was calculated using Two-way ANOVA with Sidak’s multiple comparison test, one-way ANOVA with Tukey’s multiple comparison test, or Student T-test (GraphPad Prism vs 10.3.0).

Techniques: Functional Assay, Crystal Violet Assay, Control, In Vivo, Comparison, CRISPR, Infection, Soft Agar Assay, Staining

Journal: Stem Cell Research & Therapy

Article Title: Human umbilical cord mesenchymal stem cell-derived microvesicles alleviate pulmonary fibrosis by inhibiting monocyte‒macrophage migration through ERK1/2 signaling-mediated suppression of CCL2 expression

doi: 10.1186/s13287-025-04266-w

Figure Lengend Snippet: Effects of MSC-MVs on BLM-induced PF in mice. ( a ) Diagram of the experimental scheme. ( b ) HE staining of mouse lung tissue from the control, model, and MV groups. ( c ) Ashcroft score of three groups ( n = 5). ( d - e ) Masson staining of mouse lung tissues from the three groups of mice and the statistical analysis of collagen-volume fraction %( n = 5). ( f - k ) Immunohistochemical staining of collagen I, α-SMA and FN and comparative analysis of the average optical density (AOD) were performed to assess positive staining in lung tissue ( n = 5). ( l - o ) The corresponding levels of FN, collagen I and α-SMA in the lung tissues of mice in the control, model, and MV groups were determined by WB, with GAPDH as an internal reference The corresponding uncropped full-length blots are included in Supplementary Fig. d ( n = 4). The data are shown as the means ± SEMs. The Shapiro-Wilk test of the data > 0.05. One-way ANOVA followed by the Sidak multiple comparison test was used to identify differences among the three groups, and ∗ indicates the difference between the control and model groups or the difference between the model group and the MV group. ∗∗ p < 0.01. *** p < 0.001. Scale bar, 100 μm. Abbreviations: SEM: standard error of the mean

Article Snippet: Data with unequal sample sizes were analyzed via one-way ANOVA followed by the Sidak multiple comparison test (GraphPad Prism 8.0.1), whereas for non-normally distributed data, differences between two groups were determined via the Mann‒Whitney U test for unpaired observations.

Techniques: Staining, Control, Immunohistochemical staining, Comparison

Journal: Stem Cell Research & Therapy

Article Title: Human umbilical cord mesenchymal stem cell-derived microvesicles alleviate pulmonary fibrosis by inhibiting monocyte‒macrophage migration through ERK1/2 signaling-mediated suppression of CCL2 expression

doi: 10.1186/s13287-025-04266-w

Figure Lengend Snippet: MSC-MVs inhibited monocytes and macrophages in early BLM-induced PF in mice. ( a ) Flow cytometric analysis of neutrophils, monocytes and macrophages in the peripheral blood of animals in the control, model, and MV groups. ( b - d ) Statistical analysis of the flow cytometric results of neutrophils and macrophages in the peripheral blood of the three groups. ( e - g ) The serum levels of TNF-α, IL-6, and IL10 in the three groups were measured. ( h , i ) Flow cytometric analysis of neutrophils, monocytes, macrophages, M1 macrophages and M2 macrophages in the BALF of the three groups. ( j ) Statistical analysis of the number of total cells in the BALF of the three groups. ( k - o ) Statistical analysis of the flow cytometric results for neutrophils, monocytes, macrophages, M1 macrophages and M2 macrophages in the BALF of the three groups. ( p ) IF assay showing the protein expression of F4/80 and iNOS in the lung tissue of the three groups. Scale bar = 100 μm. ( q - s ) CBD was used to measure the levels of TNF-α, IL-6, and IL-10 in the lung tissue homogenates of the three groups. n = 5. The data are shown as the means ± SEMs. The Shapiro-Wilk test of the data > 0.05. One-way ANOVA followed by the Sidak multiple comparison test was used to identify differences among the three groups, and ∗ indicates the difference between the control and model groups or the difference between the model group and the MV group. ** p < 0.01. *** p < 0.001

Article Snippet: Data with unequal sample sizes were analyzed via one-way ANOVA followed by the Sidak multiple comparison test (GraphPad Prism 8.0.1), whereas for non-normally distributed data, differences between two groups were determined via the Mann‒Whitney U test for unpaired observations.

Techniques: Control, Expressing, Comparison

Journal: Stem Cell Research & Therapy

Article Title: Human umbilical cord mesenchymal stem cell-derived microvesicles alleviate pulmonary fibrosis by inhibiting monocyte‒macrophage migration through ERK1/2 signaling-mediated suppression of CCL2 expression

doi: 10.1186/s13287-025-04266-w

Figure Lengend Snippet: MSC-MVs inhibited chemotaxis through the CCL2/CCR2 axis to regulate the chemotaxis of monocytes and macrophages. ( a ) Bubble chart of the GO enrichment of 116 genes related to monocytes and macrophages. The color of the bubbles indicates the p value, and the size of the bubbles indicates the number of genes associated with the GO term. ( b ) Bubble chart of the GO enrichment of 28 genes related to the migration of monocytes and macrophages. The color of the bubbles indicates the p value, and the size of the bubbles indicates the number of genes associated with the GO term. ( c ) Flow cytometric analysis showing CCR2 expression in monocytes and macrophages in the peripheral blood of the control, model, and MV groups. ( d , e ) Statistical analysis of the flow cytometric results showing CCR2 expression in monocytes and macrophages in the peripheral blood of the three groups ( n = 5). ( f , h ) Representative images of immunohistochemical staining for CCR2 and CCL2. ( g , i ) Comparative analysis of the AOD values showing positive staining for CCR2 and CCL2 in lung tissues ( n = 5). ( j ) Serum CCL2 protein levels in the three groups( n = 5). ( k ) CCL2 levels in the lung homogenates of the three groups( n = 5). ( l ) Confocal microscopy revealed that MHS cells take up MSCs-MVs. MHS cells were stained with CFSE (green), and MSC-MVs were stained with PKH26 (red). ( m ) CCL2 mRNA levels in MHS cells in the control, LPS and LPS + MV groups ( n = 3). ( n ) The protein level of CCL2 in the MHS cell supernatants of the control, LPS and LPS + MV groups( n = 3). ( o ) Experimental program for assessing the migration of RAW264.7 cells. ( p ) Representative images of the wound-healing assay of RAW264.7 cells in the three groups. ( q ) Comparative analysis of relative migration rates (%) in the three groups( n = 3). The data are shown as the means ± SEMs. The Shapiro-Wilk test of the data > 0.05. One-way ANOVA followed by the Sidak multiple comparison test was used to identify differences among the three groups, and * indicates a difference between the control and model groups or between the model group and the MV group. ** p < 0.01. *** p < 0.001

Article Snippet: Data with unequal sample sizes were analyzed via one-way ANOVA followed by the Sidak multiple comparison test (GraphPad Prism 8.0.1), whereas for non-normally distributed data, differences between two groups were determined via the Mann‒Whitney U test for unpaired observations.

Techniques: Chemotaxis Assay, Migration, Expressing, Control, Immunohistochemical staining, Staining, Confocal Microscopy, Wound Healing Assay, Comparison

Journal: Stem Cell Research & Therapy

Article Title: Human umbilical cord mesenchymal stem cell-derived microvesicles alleviate pulmonary fibrosis by inhibiting monocyte‒macrophage migration through ERK1/2 signaling-mediated suppression of CCL2 expression

doi: 10.1186/s13287-025-04266-w

Figure Lengend Snippet: MSC-MVs induced ERK1/2 protein phosphorylation to inhibit CCL2 expression. ( a ) Bubble chart of the GO enrichment of 62 genes related to CCL2. The color of the bubbles indicates the p value, and the size of the bubbles indicates the number of genes associated with the GO term. ( b , d ) The corresponding levels of phosphorylated ERK1/2 (p-ERK1/2) and total ERK1/2 (t-ERK1/2) in the lung tissues of mice in the control, model, and MV groups were determined by WB, with GAPDH as an internal reference. The corresponding uncropped full-length blots are included in Supplementary Fig. b ( n = 4–5). ( c , e ) The corresponding levels of p-ERK1/2 and t-ERK1/2 in the MHS cells in the control, LPS and LPS + MV groups were determined by WB with GAPDH as an internal reference. The corresponding uncropped full-length blots are included in Supplementary Fig. c ( n = 4). ( f , g ) The mRNA and protein levels of CCL2 in MHS cells in the control, LPS, LPS + MV and LPS + LY3214996 groups ( n = 3). ( H ) Representative images of the wound-healing assay of RAW264.7 cells in the four groups. ( i ) Comparative analysis of relative migration rates (%) in the four groups ( n = 3). The data are shown as the means ± SEMs. The Shapiro-Wilk test of the data > 0.05. One-way ANOVA followed by the Sidak multiple comparison test was used to identify differences among the three groups, and * indicates the difference between the control and model groups or the difference between the model group and the MV group. ** p < 0.01. *** p < 0.001

Article Snippet: Data with unequal sample sizes were analyzed via one-way ANOVA followed by the Sidak multiple comparison test (GraphPad Prism 8.0.1), whereas for non-normally distributed data, differences between two groups were determined via the Mann‒Whitney U test for unpaired observations.

Techniques: Phospho-proteomics, Expressing, Control, Wound Healing Assay, Migration, Comparison