Table S4 . (B) Scatterplot comparing changes in the chromatin accessibility of ATAC-seq peaks (x axis) with the corresponding changes in gene expression of the nearest genes (y axis). One point is indicated for each combination of differentially accessible peak (from A) and differentially expressed gene. Color indicates the mean of both fold changes. (C) The protein levels of YAP1, LAMA5, and β-actin were detected by western blot for WT MSCLCs, EF Prx1 MSCLCs, and hr-EF Prx1 MSCLCs (top) and those of Yap1 by immunofluorescence staining (bottom). Scale bars: 50 μm. (D) Bar plots showing DNA sequence motifs (mouse and human TF motifs from JASPAR 2022 ) overrepresented in peaks belonging to each of the five modules from (A). Each plot chart lists the top three motifs per module and each bar indicates the percentage of peaks with at least one match to the given motif. Enrichment was calculated using Fisher’s exact test (one-tailed). ∗ p adj < 0.05, ∗∗ p adj ≤ 0.01, and ∗∗∗ p adj ≤ 0.005. See
. (E) Left: Western blot analysis of YAP1 levels in hr-EF Prx1 MSCLCs #2 upon knockout of Yap1 using three CRISPR single-guide (sg)RNAs (sg-Yap1). Middle: Representative soft-agar assay for hr-EF Prx1 cells transduced with sg-Ctrl versus sg-Yap1. Right: The number of cell colonies was counted on days 21 after plating. Data are presented as the mean ± SE ( n = 3), ∗∗∗ p < 0.001. Statistics were calculated by one-tailed, paired Student’s t test. (F) Quantitative analysis by RT-qPCR of relative mRNA expression levels of Yap1, Igf2bp1, Hpf1, Cenpq, and Ccnd1 after knockout of Yap1. Data are presented as the mean ± SE ( n = 3), ∗∗∗ p < 0.001 and ∗∗ p < 0.001. Statistics were calculated by one-tailed, paired Student’s t test. " width="100%" height="100%">
Journal: Cell Reports
Article Title: YAP1 is a key regulator of EWS::FLI1-dependent malignant transformation upon IGF-1-mediated reprogramming of bone mesenchymal stem cells
doi: 10.1016/j.celrep.2025.115381
Figure Lengend Snippet: Comparative analysis of differentially accessible chromatin modules in MSCLCs (A) Heatmap showing row-scaled normalized read counts for all peaks that were considered differentially accessible in at least one comparison (EF Prx1 MSCLCs/WT MSCLCs, hr-EF Prx1 MSCLCs/EF Prx1 MSCLCs, or MSCLC + IGF-1/WT MSCLCs; n total = 2,038). Peaks are grouped into five “modules” (M1–M5). GGAA motif density in differentially open regions is indicated to the right of the heatmap. See Table S4 . (B) Scatterplot comparing changes in the chromatin accessibility of ATAC-seq peaks (x axis) with the corresponding changes in gene expression of the nearest genes (y axis). One point is indicated for each combination of differentially accessible peak (from A) and differentially expressed gene. Color indicates the mean of both fold changes. (C) The protein levels of YAP1, LAMA5, and β-actin were detected by western blot for WT MSCLCs, EF Prx1 MSCLCs, and hr-EF Prx1 MSCLCs (top) and those of Yap1 by immunofluorescence staining (bottom). Scale bars: 50 μm. (D) Bar plots showing DNA sequence motifs (mouse and human TF motifs from JASPAR 2022 ) overrepresented in peaks belonging to each of the five modules from (A). Each plot chart lists the top three motifs per module and each bar indicates the percentage of peaks with at least one match to the given motif. Enrichment was calculated using Fisher’s exact test (one-tailed). ∗ p adj < 0.05, ∗∗ p adj ≤ 0.01, and ∗∗∗ p adj ≤ 0.005. See Table S9 . (E) Left: Western blot analysis of YAP1 levels in hr-EF Prx1 MSCLCs #2 upon knockout of Yap1 using three CRISPR single-guide (sg)RNAs (sg-Yap1). Middle: Representative soft-agar assay for hr-EF Prx1 cells transduced with sg-Ctrl versus sg-Yap1. Right: The number of cell colonies was counted on days 21 after plating. Data are presented as the mean ± SE ( n = 3), ∗∗∗ p < 0.001. Statistics were calculated by one-tailed, paired Student’s t test. (F) Quantitative analysis by RT-qPCR of relative mRNA expression levels of Yap1, Igf2bp1, Hpf1, Cenpq, and Ccnd1 after knockout of Yap1. Data are presented as the mean ± SE ( n = 3), ∗∗∗ p < 0.001 and ∗∗ p < 0.001. Statistics were calculated by one-tailed, paired Student’s t test.
Article Snippet: LentiCRISPR Yap1 sgRNA Crispr/Cas9 all in-one lentivector set mouse , Applied Biological Materials (abm) , Cat# 505841140595.
Techniques: Comparison, Gene Expression, Western Blot, Immunofluorescence, Staining, Sequencing, One-tailed Test, Knock-Out, CRISPR, Soft Agar Assay, Transduction, Quantitative RT-PCR, Expressing
Table S4 . (B) Scatterplot comparing changes in the chromatin accessibility of ATAC-seq peaks (x axis) with the corresponding changes in gene expression of the nearest genes (y axis). One point is indicated for each combination of differentially accessible peak (from A) and differentially expressed gene. Color indicates the mean of both fold changes. (C) The protein levels of 