Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell and sub-compartment specific proteomics reveals astrocyte contributions in a mouse model of OCD

ABSTRACT: Cell and sub-compartment specific proteomics reveals astrocyte contributions in a mouse model of OCD

PROVIDER: PRJNA766219 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16071200_1.fastq.gz	Fastqsanger.gz
	SRR16071200_2.fastq.gz	Fastqsanger.gz
	SRR16071201_1.fastq.gz	Fastqsanger.gz
	SRR16071201_2.fastq.gz	Fastqsanger.gz
	SRR16071202_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 224

Similar Datasets

Cell and sub-compartment specific proteomics reveals astrocyte contributions in a mouse model of OCD

Project description:We investigated the sub-proteomes of different functional compartments in astrocyte and neurons in the striatum. We compared the proteomes to the cell-specific RNA profiles of neurons and astrocytes from these analyses. We found one gene and protein that was highly expressed in neurons and astrocytes called SAPAP3. Knockout of this gene product results in an OCD-like phenotype in mouse. RNA-seq of astrocytes and bulk RNA-seq analyses of this mouse model revealed very low DEGs.

2023-01-13 | GSE184773 | GEO

Astrocyte and neuron subcompartment proteomes reveal distinct cellular and molecular mechanisms of OCD

Project description:Astrocytes and neurons coexist and interact in the CNS1,2. Given that many signaling and pathological events are protein-driven, identifying astrocyte and neuron proteomes is essential for elucidating the complex protein networks that dictate their respective contributions to physiology and disease. Here, we used cell- and subcompartment-specific proximity-dependent biotinylation3 to study the proteomes of striatal astrocytes and medium spiny neurons (MSNs) in vivo. We evaluated cytosolic and plasma membrane compartments for astrocytes and MSNs, revealing how these cells differ at the protein level and in their core signaling machinery. We assessed subcellular compartments of astrocytes including end feet and processes to reveal the molecular basis of essential astrocyte signaling and homeostatic functions. Unexpectedly, SAPAP3 proteins (gene; Dlgap3) associated with obsessive compulsive disorder (OCD) and repetitive behaviors4-11 were detected at equivalent levels in striatal astrocyte and MSN plasma membrane and cytosolic compartments. Astrocytic expression was confirmed by RNA-seq, fluorescence in situ hybridization and immunohistochemistry. Furthermore, genetic rescue experiments combined with behavioral analyses and proteomics in a mouse model4 of OCD lacking SAPAP3 revealed contributions of SAPAP3 in astrocytes and MSNs to repetitive and anxiety-related OCD behaviors. Our data define how astrocytes and neurons differ at the protein level and in their major signaling pathways, how astrocyte proteomes vary between physiological subcompartments, and how specific astrocyte and neuronal molecular mechanisms contribute to a psychiatric disease. Targeting both astrocytes and neurons together is likely to be therapeutically effective in complex CNS disorders.

2023-01-13 | PXD029257 | Pride

Astrocyte morphology driven improvements to OCD phenotypes

Project description:We investigated the consequences of striatal astrocyte Gi-GPCR activation in the SAPAP3 KO mouse model of OCD

2024-07-09 | GSE247241 | GEO

Astrocyte-neuron contributions to Huntington’s disease dissected with ZFPs

Project description:Astrocyte-neuron contributions to Huntington’s disease dissected with ZFPs

| PRJNA783944 | ENA

Astrocyte morphology driven improvements to OCD phenotypes

Project description:Astrocyte morphology driven improvements to OCD phenotypes

| PRJNA1036677 | ENA

Proteomics of the astrocyte secretome

Project description:Proteomics of the astrocyte secretome in response to soluble oligomeric Aß

2023-05-23 | PXD036343 | Pride

Identification of Ligand-Receptor Pairs that Drive Human Astrocyte Development

Project description:We tested a group of five neuronally-secreted ligands and validated their synergistic contributions to astrocyte development within both human cortical organoids and primary fetal tissue.

2023-06-06 | GSE213245 | GEO

CscoreTool-M infers 3D sub-compartment probabilities within cell population

Project description:Motivation: Computational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods fail to address the cell population heterogeneity. Here we describe a probabilistic modeling-based method called CscoreTool-M that infers multiple 3D genome sub-compartments from Hi-C data. Results: The compartment scores inferred using CscoreTool-M represents the probability of a genomic region locating in a specific sub-compartment. Compared to published methods, CscoreTool-M is more accurate in inferring sub-compartments corresponding to both active and repressed chromatin. The compartment scores calculated by CscoreTool-M also help to quantify the levels of heterogeneity in sub-compartment localization within cell populations. By comparing proliferating cells and terminally differentiated non-proliferating cells, we show that the proliferating cells have higher genome organization heterogeneity, which is likely caused by cells at different cell-cycle stages. By analyzing 10 sub-compartments, we found a sub-compartment containing chromatin potentially related to the early-G1 chromatin regions proximal to the nuclear lamina in HCT116 cells, suggesting the method can deconvolve cell cycle stage-specific genome organization among asynchronously dividing cells. Finally, we show that CscoreTool-M can identify sub-compartments that contain genes enriched in housekeeping or cell-type-specific functions. Availability: https://github.com/scoutzxb/CscoreTool-M

2023-05-31 | GSE224282 | GEO

CscoreTool-M infers 3D sub-compartment probabilities within cell population

Project description:CscoreTool-M infers 3D sub-compartment probabilities within cell population

| PRJNA930459 | ENA

Identification of genes associated with the astrocyte-specific gene Gfap during astrocyte differentiation

Project description:Chromosomes and genes are non-randomly arranged within the mammalian cell nucleus. Clustering of genes is of great significance in transcriptional regulation. However, the relevance of gene clustering in their expression during differentiation of neural precursor cells (NPCs) into astrocytes remains unclear. We performed a genome-wide enhanced circular chromosomal conformation capture (e4C) to screen genes associated with an astrocyte-specific gene, glial fibrillary acidic protein (Gfap), during astrocyte differentiation. We identified 13 genes that were specifically associated with Gfap and expressed in NPC-derived astrocytes. These results provide evidence for functional significance of gene clustering in transcriptional regulation during NPCs differentiation. comparison of NPCs vs LIF+ vs LIF- cells.

2015-02-20 | E-GEOD-66097 | biostudies-arrayexpress

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