Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenome comparisons reveal linkage between gene expression and developmental remodeling of chromatin domain topology

ABSTRACT: We describe a new approach to ChIP-seq analysis in which conservation of nucleosome-scale H3K27me3 topology, rather than coverage, is quantified; RNA-seq results are related to the new ChIP-seq approach.

ORGANISM(S): Homo sapiens

PROVIDER: GSE94631 | GEO | 2017/03/31

SECONDARY ACCESSION(S): PRJNA371637

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology.

Project description: Not available

| S-EPMC5821309 | biostudies-literature

tsRibo-Seq: An Approach to Zoom In into Translation of Single Transcripts

Project description:Ribo-Seq (ribosome profiling) enables global assessment of translation efficiency, yields and fidelity. However, low-abundance transcripts receive little coverage and fall outside of the Ribo-Seq detection limit. We developed a new twist of the Ribo-Seq approach, termed transcript specific Ribo-Seq (tsRibo-Seq) to specifically detect lowly abundant messenger RNAs (mRNAs). This approach yields unprecedented depth in the coverage of individual low-abundance transcripts allowing identification of slow and fast translating regions with nucleotide resolution.

2020-10-03 | GSE104587 | GEO

Chromatin topology and the timing of enhancer function at the HoxD locus [ChIP-seq]

Project description:Chromatin topology and the timing of enhancer function at the HoxD locus [ChIP-seq]

| PRJNA645389 | ENA

Mass spectrometric analysis of membrane protein topology

Project description:Here we made an attempt to obtain partial structural information on the topology of multispan integral membrane proteins of yeast by isolating organellar membranes, removing peripheral membrane proteins at pH 11.5 and introducing chemical crosslinks between vicinal amino acids either using homo- or hetero-bifunctional crosslinkers. Proteins were digested with specific proteases and the products analysed by mass spectrometry. Dedicated software tools were used together with filtering steps optimized to remove false positive crosslinks. In proteins of known structure, crosslinks were found only between loops residing on the same side of the membrane. As may be expected, crosslinks were mainly found in very abundant proteins. Our approach seems to hold to promise to yield low resolution topological information for naturally very abundant or strongly overexpressed proteins with relatively little effort.

2017-10-11 | PXD006707 | Pride

Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia (ChIP-seq)

Project description:Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia (ChIP-seq)

| PRJNA596207 | ENA

Applied topology delineates developmental progression with single-cell resolution

Project description:Cellular lineage commitment and terminal cellular differentiation result from the induction of dynamically regulated transcriptional programs. We report an unbiased approach to studying this process that combines temporal single cell RNA-sequencing and topology-based computational analyses (single cell Topological Data Analysis (scTDA)). scTDA is a non-linear, model-independent, statistical framework particularly tailored to capture high-dimensional continuous relationships, allowing for unsupervised characterization of transient cellular states. We analyzed single-cell RNA-seq data from murine embryonic stem cells (mESCs) as they differentiate in vitro in response to inducers of motor neuron differentiation. scTDA resolved asynchrony and continuity in cellular identity over time, and identified four transient states (pluripotent, precursor, progenitor, and fully differentiated cells) based on dynamic changes in stage-dependent combinations of transcription factors, RNA-binding proteins and long non-coding RNAs. scTDA is applicable to a broad range of problems that involve asynchronous or stochastic cellular responses to developmental cues or environmental perturbations.

2017-02-15 | GSE94883 | GEO

In situ dissection of domain boundaries affects genome topology and gene transcription in Drosophila [RNA-seq]

Project description:In situ dissection of domain boundaries affects genome topology and gene transcription in Drosophila [RNA-seq]

| PRJNA561364 | ENA

Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (ChIP-Seq)

Project description:Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (ChIP-Seq)

| PRJNA508527 | ENA

Interplay between genome topology and gene regulation during somatic cell reprogramming [ChIP-seq]

Project description:Studies of genome topology, chromatin state and transcriptome dynamics during highly-efficient somatic cell reprogramming

2018-01-30 | GSE96548 | GEO