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Genome-wide MNase-ChIP profile of transfected Strep-LIN9 in WT and LIN37-/- HCT116 cells

ABSTRACT: Genome-wide MNase-ChIP profile of transfected Strep-LIN9 in WT and LIN37-/- HCT116 cells

PROVIDER: PRJNA783010 | ENA |

REPOSITORIES: ENA

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Genome-wide MNase-ChIP profile of transfected Strep-LIN9 in WT and LIN37-/- HCT116 cells

Project description:We performed MNase-ChIP seq with deep digestion to identify the MuvB associated nucleosomes in WT and LIN37 -/- HCT116 cells in G1 arrested and cycling cells. Strep-LIN9 as well as a mutant of the protein (Strep-4xLIN9: R174A/R175A/F180A/F181A) which is unable to associate with LIN37 or RbAP48 were transiently transfected in WT and LIN37 -/- HCT116 cells. At 24 hours after transfection, cells were treated with Nutlin-3a to induce G1 arrest; cells were harvested 48 hours following treatment. For several samples, Nutlin-3a treatment was omitted to maintain cycling conditions. Cells were then cross-linked with formaldehyde, lysed and treated with micrococcal nuclease. Chromatin fragments were precipitated with Streptactin-XT magnetic beads after which DNA was purified and libraries were prepared and sequenced using NovaSeq 6000 platform in 150bp paired-end mode. We find that LIN9 precipitates to +1 nucleosomes of target genes in arrested HCT116 and LIN37 -/- cells. The precipitation of this nucleosome is diminished in cycling cells as well as in arrested cells transfected with the Strep-4xLIN9 mutant.

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Expression profile of HCT116 cells transfected with miR-204-5p

2014-07-30 | E-GEOD-59897 | biostudies-arrayexpress

Expression of HCT116 cells transfected with CD44 siRNAs relative to that of HCT116 cells transfected with a control siRNA

Project description:To examine whether depletion of CD44 might affect antioxidant gene expression in cancer cells, HCT116 cells were transfected with CD44 or control siRNAs and subjected to cDNA microarray analysis. Although the CD44 siRNA was found to deplete the cells of CD44 mRNA, the expression of antioxidant genes was largely unaffected. HCT116 cells were transfected with CD44 or control siRNAs and subjected to cDNA microarray analysis. Two replicates per siRNA.

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The global transcriptome analysis of HCT116 cells transfected with scrambled or CBX4 shRNA

Project description:To investigate the molecular mechanism of CBX4 in CRC, the global transcriptomes were analyzed in HCT116 cells in which CBX4 was knocked down with shRNA, and these transcriptomes were compared to those of HCT116 cells transfected with scrambled shRNA.

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Expression of HCT116 cells transfected with CD44 siRNAs relative to that of HCT116 cells transfected with a control siRNA

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Expression profiling of HCT116 cells transfected with shCTRL or shKSR1

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Next Generation DNA sequencing of telomere fusion events isolated from HCT116 LIG3-/-:mL3, HCT116 LIG4-/-, WT HCT116 and MRC5HPVE6E7 cells

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