Journal: bioRxiv

Article Title: Differential sensitivity to LINE 1-induced damage contributes to the expansion of Tet2-deficient HSCs upon chronic inflammatory stress

doi: 10.1101/2025.07.21.665900

Figure Lengend Snippet: (A) GSEA analysis showing Hallmark gene sets significantly differentially enriched (padj<0.05 and -1.51.5) in WT-LPS vs WT (left) and/or in Tet2 -/- -LPS vs Tet2 -/- (right) comparisons. (B-E) Enrichment plots for E2F TARGETS (B-C) and TNF-α signalling via NF-κB (D-E) hallmark genesets in WT-LPS vs WT (B,D) and Tet2 -/- -LPS vs Tet2 -/- (C,E) conditions. NES: normalized enrichment score. (F-G) violin plot representing TE subfamilies expression for each TE subfamily significantly (p<0.05) differentially expressed in WT-LPS vs WT (F) and Tet2 -/- -LPS vs Tet2 -/- (G) conditions.

Article Snippet: For pathway enrichment analysis and data visualization, we performed Gene Set Enrichment Analysis (GSEA) using the GSEA command line (v 4.3.3, Broad Institute) ( ).

Techniques: Expressing

Journal: Cancer research

Article Title: M 6 A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression

doi: 10.1158/0008-5472.CAN-21-2106

Figure Lengend Snippet: ALKBH5 regulates DNA damage repair events in cancer cells. A, Representative dot plots showing γH2AX-positive cells in scrambled siRNA or ALKBH5 siRNA–transfected U2OS cells. U2OS cells were transfected with scrambled siRNA or ALKBH5 siRNA for 72 hours before flow cytometry analyses. Bar graph shows means ± SEM (n = 3). B, Western blots of scrambled and ALKBH5 siRNA–transfected U2OS cells using antibodies against the indicated proteins. β-Actin was used as the loading control. C, Percent of Annexin V-FITC–positive U2OS cells transfected with scrambled or ALKBH5 siRNA. D, Results of flow cytometry showing γH2AX-positive cells in scrambled siRNA and ALKBH5 siRNA–transfected 143B osteosarcoma cells. Cells were treated with no ionizing radiation (IR) or 10 Gy IR. After 24 hours, cells were stained for γH2AX to estimate unrepaired double-strand breaks. E, Bar graphs show quantification of γH2AX-positive cells shown in D. P values for A, C, and E were calculated using standard Student t tests. Bar graph represents means ± SEM (n = 3). F, GSEA showing enrichment of DNA damage repair pathway in ALKBH5 KD cells compared with scrambled siRNA–transfected 143B cells. G, Results of DR-GFP reporter assay showing DSB-induced HR repair. U2OS-DR-GFP cells were transfected with scrambled siRNA or ALKBH5 siRNAs followed by transfection with a pCAGGS vector expressing I-SceI endonuclease or empty vector as control. I-SceI endonuclease expression induces DSB if repaired by HR results in GFP+ cells as determined by flow cytometry analysis. H, EJ5-GFP reporter assay showing total NHEJ. EJ5-GFP U2OS cells were transfected with scrambled siRNA or ALKBH5 siRNAs followed by transfection with a pCAGGS vector expressing I-SceI endonuclease or empty vector as control. I-SceI endonuclease induced DSB if repaired by NHEJ results in GFP+ cells as determined by flow cytometry. For G and H, bar graphs show means ± SEM (n = 3). P values were calculated using one-way ANOVA followed by Dunnett multiple comparisons test. *, P < 0.05 **, P < 0.01; ****, P < 0.0001.

Article Snippet: Using the differential expression fold change, we also performed Gene Set Enrichment Analysis (GSEA), using the stand-alone package from the Broad Institute (v4.0.3).

Techniques: Transfection, Flow Cytometry, Western Blot, Control, Staining, Reporter Assay, Plasmid Preparation, Expressing