Journal: Bioscience, biotechnology, and biochemistry

Article Title: ARHGEF10L expression regulates cell proliferation and migration in gastric tumorigenesis.

doi: 10.1080/09168451.2020.1737503

Figure Lengend Snippet: Figure 7. Detecting HSPA6 expression in SGC7901 cells transfected with ARHGEF10L-expressing plasmids (ARHGEF10L) or blank expression vectors (Mock).

Article Snippet: The ARHGEF10L antibody was commercially obtained from Sigma; the GAPDH, N-cadherin, E-cadherin and HSPA6 antibodies from Proteintech; and the ROCK1, Slug, Phospho-Ezrin (Thr567)/Radixin (Thr564)/Moesin (Thr558) and Ezrin/Radixin/Moesin antibodies from Cell Signaling Technology (USA).

Techniques: Expressing, Transfection

Journal: Frontiers in Cell and Developmental Biology

Article Title: ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4

doi: 10.3389/fcell.2020.00553

Figure Lengend Snippet: The primers for ChIP-qPCR.

Article Snippet: Antibodies used for WB were ADNP (R&D Systems, AF5919, 1:500), FLAG (F3165, Sigma, 1:1000), HA (66006-1-Ig, Proteintech, 1:1000), BRG1 (21634-1-AP, Proteintech, 1:1000), CHD4 (ab181370, Abcam, 1:1000), SOX17 (24903-1-AP, Proteintech, 1:1000), GATA4 (19530-1-AP, Proteintech, 1:1000) and GATA6 (55435-1-AP, Proteintech, 1:1000).

Techniques:

Journal: Frontiers in Cell and Developmental Biology

Article Title: ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4

doi: 10.3389/fcell.2020.00553

Figure Lengend Snippet: The primers for qRT-qPCR.

Article Snippet: Antibodies used for WB were ADNP (R&D Systems, AF5919, 1:500), FLAG (F3165, Sigma, 1:1000), HA (66006-1-Ig, Proteintech, 1:1000), BRG1 (21634-1-AP, Proteintech, 1:1000), CHD4 (ab181370, Abcam, 1:1000), SOX17 (24903-1-AP, Proteintech, 1:1000), GATA4 (19530-1-AP, Proteintech, 1:1000) and GATA6 (55435-1-AP, Proteintech, 1:1000).

Techniques:

Journal: bioRxiv

Article Title: PB-scope: Contrastive learning of dynamic processing body formation reveals undefined mechanisms of approved compounds

doi: 10.1101/2025.06.14.659731

Figure Lengend Snippet: (a) HCT116 cells stably expressing DDX6-GFP were plated in 96-well plates, treated with 280 compounds at 10µM concentrations, and subjected to high-content imaging using the CQ1 confocal quantitative imaging system. (b) The analyzed images consist of four channels: (i) Bright-field image for cellular morphology, (ii) Mitochondrial network, (iii) Processing body, and (iv) Nucleus. Merged composite demonstrates spatial relationships between these subcellular compartments. Scale bar: 10μm. (c) Mitochondrial channels were processed through Cellpose 3.0 to generate a curated dataset containing over 400,000 high-quality single-cell images. (d) A contrastive clustering framework was implemented for unsupervised feature extraction, followed by UMAP dimensionality reduction to identify compounds with analogous mechanism-of-action (MOA) profiles through cluster localization analysis. (e) Quantitative analysis of P-body formation followed by drug treatment. (f) Mechanistic evaluation of lead compounds via imaging analysis.

Article Snippet: As primary antibodies, we used DDX6 rabbit polyclonal antibody (Proteintech, 14632-1-AP) and EDC4 mouse monoclonal antibody (Santa Cruz Biotechnology, sc-376382).

Techniques: Stable Transfection, Expressing, Imaging, Extraction

Journal: bioRxiv

Article Title: PB-scope: Contrastive learning of dynamic processing body formation reveals undefined mechanisms of approved compounds

doi: 10.1101/2025.06.14.659731

Figure Lengend Snippet: (a) A simulation model of intracellular p-body was constructed to generate synthetic p-body distributions with ground truth annotations. (b) A YOLO-v7 architecture trained on synthetic datasets was implemented for automated identification and quantitative analysis of P-body formation. (c) Example of P-body detection, achieving >95% agreement with manual annotations . (d) P-body numbers per cell in the time course under different drug treatment groups. (e) DDX6-GFP expression level (a.u.) per cell under different drug treatment groups. Error bars represent the STD of three independent analyses for d and e. (f) Quantitative analysis of P-body numbers at 6 hours post-treatment across different drug groups. (g) Quantitative analysis of DDX6 expression level (a.u.) at 6 hours post-treatment across different drug groups. The p -values were determined using the two-tailed Mann–Whitney test for f and g. The statistical significance compared with DMSO was indicated as *** P < 0.001; ** P < 0.01; * P < 0.05; ns, no significant difference. Data points that lay outside the 15% - 85% range were deemed outliers and excluded from the statistical analysis. (h, i) Mechanism of Action (MOA) profiling for drugs in Groups 1 and 3.

Article Snippet: As primary antibodies, we used DDX6 rabbit polyclonal antibody (Proteintech, 14632-1-AP) and EDC4 mouse monoclonal antibody (Santa Cruz Biotechnology, sc-376382).

Techniques: Construct, Expressing, Two Tailed Test, MANN-WHITNEY

Journal: bioRxiv

Article Title: PB-scope: Contrastive learning of dynamic processing body formation reveals undefined mechanisms of approved compounds

doi: 10.1101/2025.06.14.659731

Figure Lengend Snippet: (a) HCT116 cells were knocked down using JAK1 and JAK2 siRNA, and immunostained for P-body components DDX6 (magenta) and EDC4 (green). The nuclei were visualized with DAPI (blue). Scale bar, 10μm. (b) Quantification of P-body number per cell across three experimental groups. Statistical significance determined by an unpaired t-test was indicated as *** P < 0.001. (c) Model of JAK/STAT signaling pathway-mediated P-body regulation. JAK is activated when cytokines or growth factors bind to their respective receptors, leading to receptor dimerization, JAK and STAT phosphorylation, and subsequent transcriptional regulation. Inhibition of the pathway by knockdown of JAK1/2 leads induction of P-body formation. The JAK inhibitors identified in this work that modulate P-body formation are shown in the right panel.

Article Snippet: As primary antibodies, we used DDX6 rabbit polyclonal antibody (Proteintech, 14632-1-AP) and EDC4 mouse monoclonal antibody (Santa Cruz Biotechnology, sc-376382).

Techniques: Phospho-proteomics, Inhibition, Knockdown