Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mus musculus

ABSTRACT: Whole genome nucleosome positioning by MNase-Seq on the mouse tumor line, RMA

PROVIDER: PRJNA292329 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2149934_1.fastq.gz	Fastqsanger.gz
	SRR2149934_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Mus musculus

Project description:Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq]

| PRJNA175501 | ENA

Mus musculus

Project description:MOE430 whole mouse - mouse colon dilution series - RMA preprocessed

| PRJNA91907 | ENA

Project description:MNase does not bias nucleosome positioning

| PRJEB2854 | ENA

Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [MNase-seq]

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.

2017-02-26 | GSE70122 | GEO

Whole genome nucleosome positioning by MNase-Seq on the mouse tumor line, RMA

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.

2016-04-28 | GSE71863 | GEO

SMARCAD1 Regulates Nucleosome Positioning and Maintenance of the Naïve Pluripotent State

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.

2014-12-30 | GSE47802 | GEO

Testis expression in Mus musculus domesticus x Mus musculus musculus hybrid zone mice

Project description:We collected whole genome testis expression data from hybrid zone mice. We integrated GWAS mapping of testis expression traits and low testis weight to gain insight into the genetic basis of hybrid male sterility.

2014-12-04 | GSE61417 | GEO

Mus musculus

Project description:Nucleosome occupancy profiles in young and old mouse liver [MNase-Seq]

| PRJNA248681 | ENA

Concentration-dependent MNase-seq with yeast spike-in normalization resolves nucleosome occupancy and accessibility in human induced pluripotent stem cells (nucMACC)

Project description:Micrococcal nuclease sequencing (MNase-seq) maps nucleosome occupancy and positioning genome-wide but is sensitive to digestion conditions and lacks standardized, quantitative normalization. We developed a refined, scalable MNase-seq workflow and applied it to human induced pluripotent stem cells (hiPSCs; FUCCI-reporter line PB010.5) across a five-point MNase digestion titration (0.5, 1, 3, 6, and 10 U), with an in-house Saccharomyces cerevisiae mononucleosomal spike-in (~5% of input DNA) added for cross-sample normalization. Libraries were sequenced on two platforms (Illumina NovaSeq X, 150 bp paired-end; Illumina NextSeq 2000, 50 bp paired-end) and analyzed with the nucMACC pipeline to quantify concentration-dependent shifts between mononucleosomal and subnucleosomal fragments and to resolve the nucleosome-depleted region and +1/-1 nucleosome positioning at transcription start sites. nucMACC accessibility scores stratified nucleosomes into hyper- and hypo-accessible classes corresponding to active and repressive chromatin states.

2026-07-28 | GSE335614 | GEO