Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial Transcriptomics reveals brain regional gene expression profiles in murine model of Periventricular Heterotopia

ABSTRACT: Spatial Transcriptomics reveals brain regional gene expression profiles in murine model of Periventricular Heterotopia

PROVIDER: PRJNA1079233 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28047300_1.fastq.gz	Fastqsanger.gz
	SRR28047300_2.fastq.gz	Fastqsanger.gz
	SRR28047400_1.fastq.gz	Fastqsanger.gz
	SRR28047400_2.fastq.gz	Fastqsanger.gz
	SRR28047500_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 608

Similar Datasets

Spatial Transcriptomics reveals brain regional gene expression profiles in murine model of Periventricular Heterotopia

Project description:Periventricular Heterotopia (PH) is a malformation of cerebral cortical development characterized by the presence of neurons along the wall of lateral ventricles. The most notable neurological symptoms are seizures that usually first appear when PH becomes evident during the teenage years. Heterozygous loss of function mutations within the FLNA gene in Xq28 are the most frequent cause of familial PH, while the genotype-phenotype correlation has not been well established. We generated a mouse model of PH by conditionally deleting Flna in neural progenitors along with a Flnb null mutation. In this mouse model, periventricular neurons are predominantly generated in postnatal ages. To understand the pathogenesis of PH and the mechanism of postnatal- adult neurogenesis, we assessed transcriptomic alterations resulting from Flna and Flnb double loss of function in the ventricular/subventricular zone (V-SVZ), upper cortical layers, and periventricular neurons, respectively. This dataset reveals spatially-dependent differential gene expressions between PH and their normal control counterparts at 3 months of age.

2024-03-04 | GSE256342 | GEO

Spatial centrosome proteome of human neural cells uncovers novel interactors and disease hubs

Project description:Despite the crucial importance of the centrosome in brain development and disease, its comprehensive proteome remains uncharacterized in neural cells. Here, we used spatial proteomics to elucidate protein interaction networks at the centrosome of iPSC-derived human neural stem cells (NSCs) and neurons. Centrosome-associated proteins were largely cell-type specific, with protein hubs involved in RNA-dynamics. Analysis of neurodevelopmental disease cohorts identified a significant overrepresentation of NSC centrosome proteins with variants in patients with periventricular heterotopia (PH). Expressing the PH-associated mutant splicing factor PRPF6 reproduced the periventricular misplacement in the developing mouse brain, highlighting mis-splicing of transcripts of the MAP-kinase SAD-A at centrosomal location as essential for the phenotype. Collectively, cell-type specific centrosome interactomes explain how genetic variants in ubiquitous proteins may convey brain-specific phenotypes.

2022-06-15 | GSE201954 | GEO

Spatial centrosome proteome of human neural cells uncovers novel interactors and disease hubs

Project description:Despite the crucial importance of the centrosome in brain development and disease, its comprehensive proteome remains uncharacterized in neural cells. Here, we used spatial proteomics to elucidate protein interaction networks at the centrosome of iPSC-derived human neural stem cells (NSCs) and neurons. Centrosome-associated proteins were largely cell type-specific, with protein hubs involved in RNA dynamics. Analysis of neurodevelopmental disease cohorts identified a significant overrepresentation of NSC centrosome proteins with variants in patients with periventricular heterotopia (PH). Expressing the PH-associated mutant splicing factor PRPF6 reproduced the periventricular misplacement in the developing mouse brain, highlighting mis-splicing of transcripts of the MAP-kinase SAD-A at centrosomal location as essential for the phenotype. Collectively, cell type-specific centrosome interactomes explain how genetic variants in ubiquitous proteins may convey brain-specific phenotypes.

2022-06-22 | PXD031936 | Pride

Compound heterozygous variants in LAMC3 in association with posterior periventricular nodular heterotopia

Project description:Periventricular nodular heterotopia is a malformation of cortical development characterized by nodules of abnormally migrated neurons.

| EGAS00001004793 | EGA

Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics [spatial]

Project description:We use spatial transcriptomics to establish regional transcriptional profile of neonatal heart tissue obtained at indicated timpoints after apical resection surgery.

2021-12-20 | GSE188888 | GEO

Spatial transcriptomics of murine eyelid

Project description:Spatial transcriptomics of murine eyelid

| PRJNA1146741 | ENA

Spatial transcriptomics from murine inguinal and mesenteric lymph nodes

Project description:B cell-interacting reticular cells (BRC) form transcriptionally and topologically stable immune-interacting microenvironments that direct efficient humoral immunity. While several immune niche factors have been elucidated, the cues sustaining BRC function and topology across activation states remain unclear. Here, we employed spatial transcriptome analysis of murine ingunal and mesenteric lymph nodes to examine co-localization of distinct BRC subsets and immune cells complementing BRC-immune cell interaction analysis. Spatial analysis supported predicted feedforward BRC-immune cell circuits that sustain topologically-organized, functional niches across inflammatory states, lymphoid organs and species.

2023-03-29 | E-MTAB-12468 | biostudies-arrayexpress

Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging (spatial transcriptomics)

Project description:These data were used in the spatial transcriptomics analysis of the article titled \\"Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging\\".

2024-04-22 | E-MTAB-13991 | biostudies-arrayexpress

Spatial transcriptomics of murine eyelid

Project description:Meibomian glands (MGs) are specialized holocrine sebaceous glands embedded in the tarsal plate of the eyelids. The cell heterogeneity of MGs is not well characterized. In this study, we performed a spatial transcriptomic analysis of murine eyelid using the 10X Visium platform.

2025-01-21 | GSE274497 | GEO

Altered migratory trajectories in cerebral organoids derived from individuals with neuronal heterotopia

Project description:Malformations of the human cortex represent a major cause of disability. Mouse models with mutations in known causal genes only partially recapitulate the phenotypes and are therefore not unlimitedly suited for understanding the molecular and cellular mechanisms responsible for these conditions. Here we study periventricular heterotopia (PH) by analyzing cerebral organoids derived from induced pluripotent stem cells of patients with mutations in the cadherin receptor-ligand pair DCHS1 and FAT4 or from isogenic knock-out lines. Our results show that human cerebral organoids reproduce the cortical heterotopia associated with PH. Mutations in DCHS1 and FAT4 or knock-down of their expression cause changes in the morphology of neural progenitor cells and result in defective neuronal migration dynamics only in a subset of neurons. Single-cell RNA-sequencing data reveal a subpopulation of mutant neurons with dysregulated genes involved in axon guidance, neuronal migration and patterning. We suggest that defective neural progenitor cell (NPC) morphology and an altered navigation system in a subset of neurons underlie this form of periventricular heterotopia.

2019-03-06 | GSE124031 | GEO

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