3 research outputs found

    MOESM1 of Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia

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    Additional file 1: Figure S1. (Top) H3K4me3 peak intensity density distribution proximal to the TSS in relation to oxygen deprivation and reoxygenation. (Bottom) H3K27me3-distribution proximal to the TSS in relation to oxygen deprivation and reoxygenation. Legend: t=0: normoxia; t=8: 8 hours of hypoxia; t=24: 24 hours of hypoxia; t=+8: 8 hours of subsequent reoxygenation. These figures and underlying data have also been published in an accompanying paper [10]. Figure S2. Relation between the ratio of H3K4me3 and H3K27me3 enrichment at the transcription start site for each gene with its associated expression level at 0 hours of hypoxia (i.e. t=0, normoxia). Higher enrichment is associated with higher expression, as observed previously [46]

    Additional file 1: Figure S1. of EGR1 controls divergent cellular responses of distinctive nucleus pulposus cell types

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    Optimization of EGR1 knock-down using siRNA, A) cells were transfected with the indicated concentrations of siRNA against EGR1 mRNA (3, 30 and 100 nM). 30 nM and 100 nM showed significant (*; p < 0.05) reduction of EGR1 expression compared to siCTRL. B) Absence of off-target effects in siEGR1 treated cells. ERG1, EGR2 and EGR3 mRNA levels are depicted in siCTRL- and in siEGR1-treated cells. Only EGR1 mRNA levels were significantly reduced (*; p < 0.05). C) Sustained EGR1 knock-down: NP-nR (nR) and NP-R (R) cells were stimulated with ITS medium in the presence of control (CTRL; 30 nM) or EGR1 siRNA (EGR1; 30 nM); EGR1 protein expression was measured at 0, 2 and 48 hours post- stimulation in both cell lines. Βeta Actin (βACT) was used as loading control; the indication (t+) points to a relatively long apposition time. (TIF 59 kb