Project description:We utilized MNase-seq to profile nucleosome positions in wild type (Ax2) and ChdC null cells both in growing cells and a partially developed state (loose-mound) to study changes in nucleosome positioning and occupancy during development and the impact the deletion of ChdC an ATP-dependent chromatin remodeller has on nucleosome positioning and occupancy. As a control for MNase sequence bias we also digested naked DNA with MNase.
Project description:Genome-wide maps of nucleosome positioning in mouse ES cells with control shRNA and on Smarcad1 KD. MNase-seq data for human colo829 cells are also included.
Project description:This SuperSeries is composed of the following subset Series: GSE40910: Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq] GSE40948: Genome-wide nucleosome positioning during embryonic stem cell development [RNA-Seq] GSE40951: Genome-wide nucleosome positioning during embryonic stem cell development [ChIP-Seq] Refer to individual Series
Project description:MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase- or sonicated- ChIP-Seq data combined with either single-end or paired-end sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance to nucleR and ChIPseqR.
Project description:We have employed MNase-Seq technology to determine the nucleosome positioning across the Ly49-expressing RMA cell line. This information was compared to the default nucleosome landscape of these cells as predicted by NuPop computations to identify transcription factor binding site regions that significantly deviate from our predictions, potentially indicating an interfering role for nucleosome binding at these sites. We report that expressed Ly49 genes significantly deviate in their nucleosome coverage at AML-1a sites when compared to other, non-expressed Ly49 genes within the same sample. This information has implications for our understanding of NK cell biology, and also presents the Ly49 family as a convenient model system for discovering how various genetic and epigenetic elements impact expression state, since Ly49 genes are stochastically expressed within a given population, but have similar transcription factor requirements. It is our hope that other work on the epigenetic control of gene expression can benefit from this model system.
Project description:We knocked down AGO2 protein by RNAi in HeLaS3 human cell line. The current experiment aims at comparing nucleosome positioning in control and AGO2 knock down cells. HeLaS3 cell were cultured in DMEM. Cells were transfected with AGO2 siRNAs (or control siRNA) at day 1. On day 4 MNAse digestion of chromatin was performed. Mnase-digested chromatin DNA fragments were sequenced by paired-end DNA-seq.
