rabbit α h3k4me3  (Cell Signaling Technology Inc)

Journal: Nature Communications

Article Title: Single-cell multi-omics identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma

doi: 10.1038/s41467-025-65466-9

Figure Lengend Snippet: A Experimental schematic. Created in BioRender. Vibhakar, R. (2025) https://BioRender.com/5nsqycy . B Profile heatmap of H3K4me3, H3K27ac, and H3K27me3 -3Kb upstream and 3Kb downstream of the TSS. D458 (parent), D458IR were treated with IDH305 (7μM) or GSK321 (1μM) for 48 hours. C Annotation of percent H3K27ac, H3K4me3, and H3K27me3 increased and decreased peak occupancy in D458IR(resistant) compared to D458(parent). (Below) Increased and decreased peak occupancy in D458IR(resistant) treated with IDH305 compared to DMSO treated D458IR. D Summary of H3K4me3, H3K27ac, and H3K27me3 peak occupancy changes at the promoter and distal intergenic and intron regions. E Schematic representation of ( F and G) . Created in BioRender. Vibhakar, R. (2025) https://BioRender.com/5nsqycy . F Scatter plots of D458IR/D458 Log 2 FC ratio compared to D458IR + IDH1i/D458IR for H3K27ac (correlation coefficient = -.58, p = 2.2e−16) and G H3K27me3 (correlation coefficient = -.35, p = 5.758e-08). Two-tailed Pearson’s correlation analysis between assigned peaks in (IR/Ctrl) and (IDH1i+IR/IR). P-value represents one sample proportions test. H Scatter plots of D458IR/D458 Log 2 FC ratio of H3K4me3 compared to H3K27me3. DEGs from scRNA-seq is overlayed on gene identified peaks, red genes up and blue genes downregulated. Green box indicates increased peak occupancy for H3K4me3 and H3K27me3. I Gene set enrichment analysis of dual occupied H3K4me3/H3K27me3 peaks. The significance of enrichment is reported as(-Log10(Pval)). J Scatter plots of D458IR + IDH1i/D458IR Log 2 FC H3K4me3 compared to H3K27me3. K Genome browser view of representative gene loci from the progenitor_photoreceptor signature. Chromatin accessibility (ATAC-seq), H3K4me3, H3K27ac, H3K27me3 occupancy in D458 (sensitive), D458IR (IR-resistant), D458IR (IR-resistant) + IDH305 (7μM) or + GSK321 (1μM) are displayed. Scale for each histone mark is shown. All CUT and RUN experiments represent a n = 2. See also Supplementary Fig. .

Article Snippet: Antibodies against α-H3K4me3 and IgG controls were validated antibodies from EpiCypher. α-H3K27me3 (Cell Signaling technologies, #9733) and α-H3K27ac (Cell signaling technologies, #8173).

Techniques: Two Tailed Test

Journal: Nature Communications

Article Title: Single-cell multi-omics identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma

doi: 10.1038/s41467-025-65466-9

Figure Lengend Snippet: A Experimental schematic. Created in BioRender. Vibhakar, R. (2025) https://BioRender.com/5nsqycy . B Profile heatmap of H3K4me3, H3K27ac, and H3K27me3 -3Kb upstream and 3Kb downstream of the TSS. D458 (parent), D458IR were treated with IDH305 (7μM) or GSK321 (1μM) for 48 hours. C Annotation of percent H3K27ac, H3K4me3, and H3K27me3 increased and decreased peak occupancy in D458IR(resistant) compared to D458(parent). (Below) Increased and decreased peak occupancy in D458IR(resistant) treated with IDH305 compared to DMSO treated D458IR. D Summary of H3K4me3, H3K27ac, and H3K27me3 peak occupancy changes at the promoter and distal intergenic and intron regions. E Schematic representation of ( F and G) . Created in BioRender. Vibhakar, R. (2025) https://BioRender.com/5nsqycy . F Scatter plots of D458IR/D458 Log 2 FC ratio compared to D458IR + IDH1i/D458IR for H3K27ac (correlation coefficient = -.58, p = 2.2e−16) and G H3K27me3 (correlation coefficient = -.35, p = 5.758e-08). Two-tailed Pearson’s correlation analysis between assigned peaks in (IR/Ctrl) and (IDH1i+IR/IR). P-value represents one sample proportions test. H Scatter plots of D458IR/D458 Log 2 FC ratio of H3K4me3 compared to H3K27me3. DEGs from scRNA-seq is overlayed on gene identified peaks, red genes up and blue genes downregulated. Green box indicates increased peak occupancy for H3K4me3 and H3K27me3. I Gene set enrichment analysis of dual occupied H3K4me3/H3K27me3 peaks. The significance of enrichment is reported as(-Log10(Pval)). J Scatter plots of D458IR + IDH1i/D458IR Log 2 FC H3K4me3 compared to H3K27me3. K Genome browser view of representative gene loci from the progenitor_photoreceptor signature. Chromatin accessibility (ATAC-seq), H3K4me3, H3K27ac, H3K27me3 occupancy in D458 (sensitive), D458IR (IR-resistant), D458IR (IR-resistant) + IDH305 (7μM) or + GSK321 (1μM) are displayed. Scale for each histone mark is shown. All CUT and RUN experiments represent a n = 2. See also Supplementary Fig. .

Article Snippet: Antibodies against α-H3K4me3 and IgG controls were validated antibodies from EpiCypher. α-H3K27me3 (Cell Signaling technologies, #9733) and α-H3K27ac (Cell signaling technologies, #8173).

Techniques: Two Tailed Test