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matlab code msdanalyzer  (MathWorks Inc)


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    MathWorks Inc matlab code msdanalyzer
    TEAD1 transcription factor stabilizes YAP condensate (A) Representative 2D confocal immunofluorescence image of a U-2 OS YAP-HaloTag cell plated sparsely, showing both YAP and TEAD1 foci. Magnification of the inset in the merged image. Scale bar: 5 μm. (B) Line scan of the dotted line in the magnified image from (A) showing the overlap of YAP and TEAD1 condensates. (C) Quantification of colocalization between YAP condensates with TEAD1 foci using Mander’s <t>coefficient.</t> ∗∗∗∗: statistically significant difference between YAP condensate/TEAD1 foci colocalization and random nuclear region/TEAD1 foci colocalization ( p < 0.0001, unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (D–M). Live-cell 2D Airyscan images of sparsely plated U-2 OS YAP-HaloTag cells treated with DMSO (D), 50 nM verteporfin (F), 500 nM K-975 (H), 500 nM Peptide 17 (J), and 500 nM CA3 (L) at the indicated time after treatment. Scale bars: 5 μm. Quantification of the YAP condensate numbers in 2D in (E, G, I, K, M) after treatment with each drug at the indicated time. ∗, ∗∗, ∗∗∗: statistically significant differences in the YAP condensate number between pre-treatment and drug-treated samples (∗: p < 0.05, ∗∗: p < 0.01, ∗∗∗: p < 0.001, paired t test). ns: non-significant difference between samples (paired t test). The center of the data is the mean and the error bars show the s.e.m. The average number of condensates during pre-treatment is higher than calculated in <xref ref-type=Figure 1 since only cells containing at least one YAP condensate were analyzed for drug treatments. (N) Normalized number of YAP condensates in 2D in sorbitol-treated, sparsely plated U-2 OS YAP-HaloTag cells per nuclear area, with additional DMSO or Peptide 17 treatments over 1 h. ∗∗, ∗∗∗, ∗∗∗∗: statistically significant difference in the YAP condensate number between DMSO and Peptide 17-treated samples at indicated time points (∗∗: p < 0.01, ∗∗∗: p < 0.001, ∗∗∗∗: p < 0.0001. Unpaired t test). ns: non-significant difference between samples at 0 min (unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (O) Differential Interference Contrast (DIC) images of purified TEAD1 (20 μM) and YAP (15 μM) proteins alone, TEAD1 (15 μM) with crowding agent 20% (w/w) PEG 2k, and TEAD1 (15 μM) and YAP (15 μM) mixed together, showing that mixing of YAP and TEAD1 promotes the phase separation of both proteins. Scale bar is 20 μm. " width="250" height="auto" />
    Matlab Code Msdanalyzer, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "YAP condensates are highly organized hubs"

    Article Title: YAP condensates are highly organized hubs

    Journal: iScience

    doi: 10.1016/j.isci.2024.109927

    TEAD1 transcription factor stabilizes YAP condensate (A) Representative 2D confocal immunofluorescence image of a U-2 OS YAP-HaloTag cell plated sparsely, showing both YAP and TEAD1 foci. Magnification of the inset in the merged image. Scale bar: 5 μm. (B) Line scan of the dotted line in the magnified image from (A) showing the overlap of YAP and TEAD1 condensates. (C) Quantification of colocalization between YAP condensates with TEAD1 foci using Mander’s coefficient. ∗∗∗∗: statistically significant difference between YAP condensate/TEAD1 foci colocalization and random nuclear region/TEAD1 foci colocalization ( p < 0.0001, unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (D–M). Live-cell 2D Airyscan images of sparsely plated U-2 OS YAP-HaloTag cells treated with DMSO (D), 50 nM verteporfin (F), 500 nM K-975 (H), 500 nM Peptide 17 (J), and 500 nM CA3 (L) at the indicated time after treatment. Scale bars: 5 μm. Quantification of the YAP condensate numbers in 2D in (E, G, I, K, M) after treatment with each drug at the indicated time. ∗, ∗∗, ∗∗∗: statistically significant differences in the YAP condensate number between pre-treatment and drug-treated samples (∗: p < 0.05, ∗∗: p < 0.01, ∗∗∗: p < 0.001, paired t test). ns: non-significant difference between samples (paired t test). The center of the data is the mean and the error bars show the s.e.m. The average number of condensates during pre-treatment is higher than calculated in <xref ref-type=Figure 1 since only cells containing at least one YAP condensate were analyzed for drug treatments. (N) Normalized number of YAP condensates in 2D in sorbitol-treated, sparsely plated U-2 OS YAP-HaloTag cells per nuclear area, with additional DMSO or Peptide 17 treatments over 1 h. ∗∗, ∗∗∗, ∗∗∗∗: statistically significant difference in the YAP condensate number between DMSO and Peptide 17-treated samples at indicated time points (∗∗: p < 0.01, ∗∗∗: p < 0.001, ∗∗∗∗: p < 0.0001. Unpaired t test). ns: non-significant difference between samples at 0 min (unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (O) Differential Interference Contrast (DIC) images of purified TEAD1 (20 μM) and YAP (15 μM) proteins alone, TEAD1 (15 μM) with crowding agent 20% (w/w) PEG 2k, and TEAD1 (15 μM) and YAP (15 μM) mixed together, showing that mixing of YAP and TEAD1 promotes the phase separation of both proteins. Scale bar is 20 μm. " title="... between YAP condensates with TEAD1 foci using Mander’s coefficient. ∗∗∗∗: statistically significant difference between YAP condensate/TEAD1 foci ..." property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: TEAD1 transcription factor stabilizes YAP condensate (A) Representative 2D confocal immunofluorescence image of a U-2 OS YAP-HaloTag cell plated sparsely, showing both YAP and TEAD1 foci. Magnification of the inset in the merged image. Scale bar: 5 μm. (B) Line scan of the dotted line in the magnified image from (A) showing the overlap of YAP and TEAD1 condensates. (C) Quantification of colocalization between YAP condensates with TEAD1 foci using Mander’s coefficient. ∗∗∗∗: statistically significant difference between YAP condensate/TEAD1 foci colocalization and random nuclear region/TEAD1 foci colocalization ( p < 0.0001, unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (D–M). Live-cell 2D Airyscan images of sparsely plated U-2 OS YAP-HaloTag cells treated with DMSO (D), 50 nM verteporfin (F), 500 nM K-975 (H), 500 nM Peptide 17 (J), and 500 nM CA3 (L) at the indicated time after treatment. Scale bars: 5 μm. Quantification of the YAP condensate numbers in 2D in (E, G, I, K, M) after treatment with each drug at the indicated time. ∗, ∗∗, ∗∗∗: statistically significant differences in the YAP condensate number between pre-treatment and drug-treated samples (∗: p < 0.05, ∗∗: p < 0.01, ∗∗∗: p < 0.001, paired t test). ns: non-significant difference between samples (paired t test). The center of the data is the mean and the error bars show the s.e.m. The average number of condensates during pre-treatment is higher than calculated in Figure 1 since only cells containing at least one YAP condensate were analyzed for drug treatments. (N) Normalized number of YAP condensates in 2D in sorbitol-treated, sparsely plated U-2 OS YAP-HaloTag cells per nuclear area, with additional DMSO or Peptide 17 treatments over 1 h. ∗∗, ∗∗∗, ∗∗∗∗: statistically significant difference in the YAP condensate number between DMSO and Peptide 17-treated samples at indicated time points (∗∗: p < 0.01, ∗∗∗: p < 0.001, ∗∗∗∗: p < 0.0001. Unpaired t test). ns: non-significant difference between samples at 0 min (unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (O) Differential Interference Contrast (DIC) images of purified TEAD1 (20 μM) and YAP (15 μM) proteins alone, TEAD1 (15 μM) with crowding agent 20% (w/w) PEG 2k, and TEAD1 (15 μM) and YAP (15 μM) mixed together, showing that mixing of YAP and TEAD1 promotes the phase separation of both proteins. Scale bar is 20 μm.

    Techniques Used: Immunofluorescence, Purification



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    matlab code msdanalyzer  (MathWorks Inc)
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    TEAD1 transcription factor stabilizes YAP condensate (A) Representative 2D confocal immunofluorescence image of a U-2 OS YAP-HaloTag cell plated sparsely, showing both YAP and TEAD1 foci. Magnification of the inset in the merged image. Scale bar: 5 μm. (B) Line scan of the dotted line in the magnified image from (A) showing the overlap of YAP and TEAD1 condensates. (C) Quantification of colocalization between YAP condensates with TEAD1 foci using Mander’s coefficient. ∗∗∗∗: statistically significant difference between YAP condensate/TEAD1 foci colocalization and random nuclear region/TEAD1 foci colocalization ( p < 0.0001, unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (D–M). Live-cell 2D Airyscan images of sparsely plated U-2 OS YAP-HaloTag cells treated with DMSO (D), 50 nM verteporfin (F), 500 nM K-975 (H), 500 nM Peptide 17 (J), and 500 nM CA3 (L) at the indicated time after treatment. Scale bars: 5 μm. Quantification of the YAP condensate numbers in 2D in (E, G, I, K, M) after treatment with each drug at the indicated time. ∗, ∗∗, ∗∗∗: statistically significant differences in the YAP condensate number between pre-treatment and drug-treated samples (∗: p < 0.05, ∗∗: p < 0.01, ∗∗∗: p < 0.001, paired t test). ns: non-significant difference between samples (paired t test). The center of the data is the mean and the error bars show the s.e.m. The average number of condensates during pre-treatment is higher than calculated in <xref ref-type=Figure 1 since only cells containing at least one YAP condensate were analyzed for drug treatments. (N) Normalized number of YAP condensates in 2D in sorbitol-treated, sparsely plated U-2 OS YAP-HaloTag cells per nuclear area, with additional DMSO or Peptide 17 treatments over 1 h. ∗∗, ∗∗∗, ∗∗∗∗: statistically significant difference in the YAP condensate number between DMSO and Peptide 17-treated samples at indicated time points (∗∗: p < 0.01, ∗∗∗: p < 0.001, ∗∗∗∗: p < 0.0001. Unpaired t test). ns: non-significant difference between samples at 0 min (unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (O) Differential Interference Contrast (DIC) images of purified TEAD1 (20 μM) and YAP (15 μM) proteins alone, TEAD1 (15 μM) with crowding agent 20% (w/w) PEG 2k, and TEAD1 (15 μM) and YAP (15 μM) mixed together, showing that mixing of YAP and TEAD1 promotes the phase separation of both proteins. Scale bar is 20 μm. " width="100%" height="100%">

    Journal: iScience

    Article Title: YAP condensates are highly organized hubs

    doi: 10.1016/j.isci.2024.109927

    Figure Lengend Snippet: TEAD1 transcription factor stabilizes YAP condensate (A) Representative 2D confocal immunofluorescence image of a U-2 OS YAP-HaloTag cell plated sparsely, showing both YAP and TEAD1 foci. Magnification of the inset in the merged image. Scale bar: 5 μm. (B) Line scan of the dotted line in the magnified image from (A) showing the overlap of YAP and TEAD1 condensates. (C) Quantification of colocalization between YAP condensates with TEAD1 foci using Mander’s coefficient. ∗∗∗∗: statistically significant difference between YAP condensate/TEAD1 foci colocalization and random nuclear region/TEAD1 foci colocalization ( p < 0.0001, unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (D–M). Live-cell 2D Airyscan images of sparsely plated U-2 OS YAP-HaloTag cells treated with DMSO (D), 50 nM verteporfin (F), 500 nM K-975 (H), 500 nM Peptide 17 (J), and 500 nM CA3 (L) at the indicated time after treatment. Scale bars: 5 μm. Quantification of the YAP condensate numbers in 2D in (E, G, I, K, M) after treatment with each drug at the indicated time. ∗, ∗∗, ∗∗∗: statistically significant differences in the YAP condensate number between pre-treatment and drug-treated samples (∗: p < 0.05, ∗∗: p < 0.01, ∗∗∗: p < 0.001, paired t test). ns: non-significant difference between samples (paired t test). The center of the data is the mean and the error bars show the s.e.m. The average number of condensates during pre-treatment is higher than calculated in Figure 1 since only cells containing at least one YAP condensate were analyzed for drug treatments. (N) Normalized number of YAP condensates in 2D in sorbitol-treated, sparsely plated U-2 OS YAP-HaloTag cells per nuclear area, with additional DMSO or Peptide 17 treatments over 1 h. ∗∗, ∗∗∗, ∗∗∗∗: statistically significant difference in the YAP condensate number between DMSO and Peptide 17-treated samples at indicated time points (∗∗: p < 0.01, ∗∗∗: p < 0.001, ∗∗∗∗: p < 0.0001. Unpaired t test). ns: non-significant difference between samples at 0 min (unpaired t test). The center of the data is the mean and the error bars show the s.e.m. (O) Differential Interference Contrast (DIC) images of purified TEAD1 (20 μM) and YAP (15 μM) proteins alone, TEAD1 (15 μM) with crowding agent 20% (w/w) PEG 2k, and TEAD1 (15 μM) and YAP (15 μM) mixed together, showing that mixing of YAP and TEAD1 promotes the phase separation of both proteins. Scale bar is 20 μm.

    Article Snippet: Diffusion coefficient calculation: MATLAB code msdanalyzer along with custom MATLAB codes were used.

    Techniques: Immunofluorescence, Purification