Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In-situ cell-type specific chromatin topologies in the brain revealed by genome architecture mapping

ABSTRACT: In-situ cell-type specific chromatin topologies in the brain revealed by genome architecture mapping

PROVIDER: PRJNA625732 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR11555700.fastq.gz	Fastqsanger.gz
	SRR11555800.fastq.gz	Fastqsanger.gz
	SRR11555900.fastq.gz	Fastqsanger.gz
	SRR11556000.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1803

Similar Datasets

In-situ cell-type specific chromatin topologies in the brain revealed by genome architecture mapping

Project description:We report the application of genome architecture mapping in specific cell types in mouse brain. We generated cell-type specific chromatin contact maps in mouse dopaminergic neurons from the midbrain ventral tegmental area (VTA DN), pyramidal glutamatergic neurons from the cornus ammonis 1 region of the hippocampus (CA1 PGN), and non-neuronal post-mitotic oligodendrocytes from the somatosensory cortex (SSC_Olig). We explored cell-type specific chromatin topologies genome-wide at multiple genomic scales. Our data demonstrates that chromatin organization is cell type specific and reflects cell specialization at all genomic scales.

2021-08-27 | GSE148792 | GEO

In-situ cell-type specific chromatin topologies in the brain revealed by genome architecture mapping [ATAC-seq]

Project description:In-situ cell-type specific chromatin topologies in the brain revealed by genome architecture mapping [ATAC-seq]

| PRJNA728375 | ENA

In-situ cell-type specific chromatin topologies in the brain revealed by genome architecture mapping [ATAC-seq]

2021-08-27 | GSE174024 | GEO

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

Project description:Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

| PRJNA322612 | ENA

Mapping separase-mediated cleavage in situ

Project description:Mapping separase-mediated cleavage in situ

| PRJNA892129 | ENA

In Situ Structural Restraints from Crosslinking Mass Spectrometry in Human Mitochondria

Project description:The field of structural biology is increasingly focusing on studying proteins in situ, i.e. in a larger biological context. Crosslinking mass spectrometry is contributing to this effort, typically through the use of MS-cleavable crosslinkers. Here, we apply the popular non-cleavable crosslinker disuccinimidyl suberate to mitochondria and identify 5,518 distance restraints between protein residues. Each distance restraint within or between proteins provides structural information on proteins and their processes within mitochondria. Comparing these restraints to high-throughput comparative models and PDB deposited structures reveals novel protein conformations. Our data suggest substrates and flexibility of mitochondrial heat shock proteins. Crosslinking mass spectrometry is progressing towards large-scale in situ structural biology that reveals protein dynamics in addition to protein-protein interaction topologies.

2019-12-03 | PXD014675 | Pride

Diploid genome architecture revealed by multi-omic data of hybrid mice

Project description:Diploid genome architecture revealed by multi-omic data of hybrid mice

| PRJNA549427 | ENA

In Situ Proximity Labeling Identifies Lewy Pathology Molecular Interactions in the Human Brain

Project description:The intracellular misfolding and accumulation of alpha-synuclein into structures collectively called LP is a central phenomenon for the pathogenesis of synucleinopathies including Parkinson’s disease (PD) and Dementia with Lewy Bodies (DLB). Understanding the molecular architecture of LP is crucial for understanding synucleinopathy disease origins and progression. Here we used a technique called biotinylation by antibody recognition (BAR) to label total (BAR-SYN1) and pathological alpha-synuclein (BAR-PSER129) in situ for subsequent mass spectrometry analysis. This technique has broad potential to help understand the phenomenon of LP in primary human tissue and animal models.

2022-02-22 | PXD028830 | Pride

Architecture of cognitive flexibility revealed by lesion mapping.

Project description:Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n=149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism-Extraversion-Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R(2)=0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence.

| S-EPMC3790579 | biostudies-literature

Transcriptome Architecture of Adult Mouse Brain Revealed by Sparse Coding of Genome-Wide In Situ Hybridization Images.

Project description:Highly differentiated brain structures with distinctly different phenotypes are closely correlated with the unique combination of gene expression patterns. Using a genome-wide in situ hybridization image dataset released by Allen Mouse Brain Atlas, we present a data-driven method of dictionary learning and sparse coding. Our results show that sparse coding can elucidate patterns of transcriptome organization of mouse brain. A collection of components obtained from sparse coding display robust region-specific molecular signatures corresponding to the canonical neuroanatomical subdivisions including fiber tracts and ventricular systems. Other components revealed finer anatomical delineation of domains previously considered homogeneous. We also build an open-access informatics portal that contains the detail of each component along with its ontology and expressed genes. This portal allows intuitive visualization, interpretation and explorations of the transcriptome architecture of a mouse brain.

| S-EPMC5540769 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data