saponin perm buffer click it plus edu alexa 647 flow cytometry assay kit cat c10634 thermo fisher scientific  (Thermo Fisher)

Journal: EMBO Molecular Medicine

Article Title: CDK12/CDK13 inhibition disrupts transcriptional elongation and replication fork progression in glioblastoma

doi: 10.1038/s44321-026-00393-w

Figure Lengend Snippet: ( A ) Dose-response curves from MTT assays for eleven high-grade glioblastoma and seven non-glioblastoma cell lines treated with THZ531. Data represent mean ± SD of three replicates. ( B ) Bar graph showing IC50 values from the MTT assays in ( A ). Statistical analyses confirm that the IC50 values for GSCs are significantly different from those of non-GSC cells. Data were analyzed by the Mann–Whitney t -test. ( C ) In vitro cell proliferation assay of the GSCs G7 and G144, and HeLa cells treated as indicated. Data represent mean ± SD of three replicates. Data were analyzed by two-way ANOVA followed by Tukey’s multiple comparisons test. Exact p values are provided in Appendix Table . ( D ) Clonogenic survival assay of G7, G144, and HeLa cells treated as indicated. ( E ) Immuno-blot analyses from G7, G144, and HeLa cells that were treated with DMSO, 500 nM THZ531 for 6, 24, and 48 h to assess total and cleaved PARP as a marker of apoptosis, with Vinculin used as a loading control. ( F ) Flow cytometry quantification of the TUNEL assay showing the percentage of apoptotic G7 cells treated with 500 nM THZ531 for 6 and 24 h. ( G ) Competition assays of sgRNAs targeting CDK9, CDK12 and CDK13, as well as positive controls (essential genes, MCM2 and RPS19). Non-targeting sgRNA (NC) was used as a negative control. Data were analyzed by two-way ANOVA followed by Tukey’s multiple comparisons test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001, significant differences as compared to the day 0. Exact p values are provided in Appendix Table . .

Article Snippet: Click-iT Plus EdU Alexa Fluor 594 Flow Cytometry Assay Kit , Fisher Scientific , C10646.

Techniques: MANN-WHITNEY, In Vitro, Proliferation Assay, Clonogenic Cell Survival Assay, Marker, Control, Flow Cytometry, TUNEL Assay, Negative Control

Journal: EMBO Molecular Medicine

Article Title: CDK12/CDK13 inhibition disrupts transcriptional elongation and replication fork progression in glioblastoma

doi: 10.1038/s44321-026-00393-w

Figure Lengend Snippet: ( A ) Venn diagrams illustrating the overlap in the populations of genes being downregulated (left) as well as upregulated (right) in G7 cells compared to G144 cells. ( B ) Graphs illustrates the moving average of transcriptional changes in nascent (top) or steady-state (middle, bottom) transcripts from G7 (top, middle) or G144 (bottom) cells treated with THZ531 for 6 h compared to DMSO controls. Transcripts were ordered according to the previously published classification of cell-cycle timing. Only transcripts, for which transcriptional timing could be assessed with an FDR-value of 0.001 or better, were included. ( C ) Beeswarm plots of transcriptional changes as in ( B ), with transcripts grouped into six overall groups based on previously published transcriptional timing. P values were obtained using Mann–Whitney U -tests and Bonferroni-corrected for multiple testing. ( D ) Bar diagrams of cell cycle distributions of G7 and G144 cells treated as indicated. Doses used: THZ531 (500 nM), Nocodazole (1 μg/mL). ( E ) Flow cytometry analysis of % of G7 cells in mitosis following 500 nM THZ531 ± 1 μg/mL Nocodazole treatment for 24 h. Data were analyzed by one-way ANOVA followed by Dunnett’s post hoc test * p < 0.05, *** p < 0.001. Significant differences as compared to the control: DMSO 18 h + NOC 6 h: p = 0.0004; THZ531 24 h: p = 0.0194; THZ531 18 h + NOC 6 h: p = 0.0231. Data represent mean ± SD of two replicates for ( D , E ). ( F ) Flow cytometric assays of γH2AX accumulation in G7 cells treated with 500 nM THZ531 for 6 and 24 h. ( G ) Cells were treated with 500 nM THZ531 at indicated times, and EdU incorporation was performed in the last 1 h by adding 10 μM EdU. Cell staining was done using Click-IT chemistry according to the manufacturer’s instructions. Scale bar: ~50 μm (approximated based on a comparable image acquired using the same imaging setup).

Article Snippet: Click-iT Plus EdU Alexa Fluor 594 Flow Cytometry Assay Kit , Fisher Scientific , C10646.

Techniques: MANN-WHITNEY, Flow Cytometry, Control, Staining, Imaging

Journal: Breast Cancer Research : BCR

Article Title: BHLHE22, targeted by deubiquitinating enzyme OTUD3, exerts an antitumor role in triple-negative breast cancer progression via transcriptionally inhibiting CDT1

doi: 10.1186/s13058-025-02198-0

Figure Lengend Snippet: mRNA-seq analysis identifies downstream target genes of BHLHE22. a , b The results of 2D and 3D principal component analysis (PCA) of the sequenced samples. c Taking |log2(fold change)|≥ 2 and p value < 0.001 as thresholds, the volcano map showed the differential expression of genes in BHLHE22-overexpressed cells. d The Cluego network diagram showed that the enriched functions of these differentially expressed gene (DEGs). e KEGG enrichment analysis of DEGs was shown by bubble map. f The link and overlapping of associated molecules among proliferation-related terms were presented as Cluego network diagram. g The Venn diagram showed overlapping genes in these four terms. h The expression of overlapping genes in BHLHE22-overexpressed cells and control cells was shown with heat maps

Article Snippet: DNA replication in the cells was detected using the EdU cell proliferation assay kit (cat. E-CK-A370, Elabscience, China).

Techniques: Quantitative Proteomics, Expressing, Control