7 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]

    HT-FC allows intratumoral analysis of stromal and cancer cell subsets within primary ccRCC samples.

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    <p>(<b>A</b>) Heatmap showing expression of each of the 363 antibodies in four subpopulations of ccRCC samples: CD45<sup>+</sup> immune cells, CD45<sup>−</sup>CD31<sup>+</sup>CD34<sup>+</sup> vascular endothelial cells, CD45<sup>−</sup>TE7<sup>+</sup> fibroblasts, and CD45<sup>−</sup>TE7<sup>−</sup>CD31<sup>−</sup>CD34<sup>−</sup> cancer cells. Antibodies are simply arranged in alphabetical order on the vertical axis and the four populations for each sample are ordered across the top. A low resolution overview demonstrates a surprisingly reproducible “fingerprint” of tumor cell subpopulations from one sample to the next. (<b>B</b>) Supervised hierarchical clustering reveals clusters of antigens corresponding to specific cell subsets within tumors (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105602#pone.0105602.s011" target="_blank">Table S6</a> for details). (<b>C</b>) Principal components analysis of the entire data set further illustrates how effectively the cell surface profile delineates the 4 distinct cell populations within primary ccRCC samples. Red: immune cells; Green: endothelial cells; Blue: fibroblasts; Orange: cancer cells.</p

    HT-FC allows phenotypic segregation and identification of cell samples from diverse lineages.

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    <p>Unsupervised hierarchical clustering of percent-positive marker expression values generated on 119 samples was performed. Colours indicate emergence of biologically related samples into clusters based on surface marker profiles. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105602#pone.0105602.s002" target="_blank">Figure S2</a> for a magnified image of the dendrogram.</p