Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial transcriptomics of P35 septum

ABSTRACT: Purpose: The goal of this study is to use MERFISH to identify the spatial distribution of septal cells Methods: P35 CD1 mice were collected.10 µm tissue sections were obtained from along the rostro-caudal axis and adhered to the MERSCOPE Slide. The samples were permeabilized in 70% ethanol overnight, followed by cell boundary staining. A 500-gene panel was generated based on enriched genes in each astrocyte and neuron cluster, with approximately 100 astrocyte genes and 400 neuron genes, The samples were then hybridized using the gene panel mix, followed by gel embedding and clearing steps. Images were processed using the MERSCOPE instrument and analysis computer, along with MERSCOPE visualizer software to streamline the acquisition of high-quality MERFISH data accroding to Vizgen; Results: Neurons and astrocytespatial clusters were defined in the septum based on unique gene enrichment

ORGANISM(S): Mus musculus synthetic construct

PROVIDER: GSE282127 | GEO | 2025/04/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Young and Aged Striatal Astrocyte MERFISH Panel

Project description:Young and Aged Striatal Astrocyte MERFISH Panel

| PRJNA1090141 | ENA

Spatial transcriptomics of P35 septum

Project description:Spatial transcriptomics of P35 septum

| PRJNA1187250 | ENA

Young and Aged Striatal Astrocyte MERFISH Panel

Project description:Given that the striatum is a large, multifunctional nucleus, we next aimed to understand where astrocyte subtypes exist in the striatum at a single-cell resolution using MERFISH. We reproducibly identified the seven astrocyte subtypes, some of which were dorsal (A1, A7), medial (A3, A6) or ventral dominant (A4).

2024-10-03 | GSE262083 | GEO

Dynamic extrinsic pacing of the HOX clock in human axial progenitors control motor neuron subtype specification

Project description:Rostro-caudal patterning of vertebrates depends on the temporally progressive activation of HOX genes within axial stem cells that fuel axial embryo elongation. Whether HOX genes sequential activation, the “HOX clock”, is paced by intrinsic chromatin-based timing mechanisms or by temporal changes in extrinsic cues remains unclear. Here, we studied HOX clock pacing in human pluripotent stem cells differentiating into spinal cord motor neuron subtypes which are progenies of axial progenitors. We show that the progressive activation of caudal HOX genes is controlled by a dynamic increase in FGF signaling. Blocking FGF pathway stalled induction of HOX genes, while precocious increase in FGF alone, or with GDF11 ligand, accelerated the HOX clock. Cells differentiated under accelerated HOX induction generated appropriate posterior motor neuron subtypes found along the human embryonic spinal cord. The HOX clock is thus dynamically paced by exposure parameters to secreted cues. Its manipulation by extrinsic factors alleviates temporal requirements to provide unprecedented synchronized access to human cells of multiple, defined, rostro-caudal identities for basic and translational applications.

2021-03-02 | GSE153519 | GEO

Mitochondrial reprogramming using dCas9 boosts glia-to-neuron conversion

Project description:Astrocyte-to-neuron conversion has developed into a promising avenue for neuronal replacement therapy. Neurons depend critically on mitochondria function and often die by ferroptosis during the conversion process. Here we examined the extent of adequate mitochondrial reprogramming by morphology and proteome analysis. While mitochondria profoundly changed their morphology during Neurogenin2 (Neurog2) – or Achaete-scute homolog 1 (Ascl1)-mediated astrocyte-to-neuron reprogramming, we found neuron-specific mitochondrial proteins, here identified in a comprehensive proteome analysis of isolated mitochondria from primary neurons and astrocytes, to be only partially and at late stages regulated during the process. To improve this, we used dCas9 technology to induce neuron-specific mitochondrial proteins early during reprogramming. This resulted not only in increased conversion efficiency, but also in faster neuronal generation. Taken together, reprogramming mitochondria in a cell type-specific manner has powerful effects on astrocyte-to-neuron conversion, suggesting mitochondria to be a driving force in this process.

2021-03-29 | PXD014886 | Pride

Astrocyte-encoded positional cues maintain sensorimotor circuit integrity

Project description:Astrocytes, the most abundant cells in the central nervous system, promote synapse formation and help refine neural connectivity. Although they are allocated to spatially distinct regional domains during development, it is unknown whether region-restricted astrocytes are functionally heterogeneous. Here we show that postnatal spinal cord astrocytes express several region-specific genes, and that ventral astrocyte-encoded Semaphorin3a (Sema3a) is required for proper motor neuron and sensory neuron circuit organization. Loss of astrocyte-encoded Sema3a led to dysregulated α−motor neuron axon initial segment orientation, markedly abnormal synaptic inputs, and selective death of α−but not of adjacent γ−motor neurons. Additionally, a subset of TrkA+ sensory afferents projected to ectopic ventral positions. These findings demonstrate that stable maintenance of a positional cue by developing astrocytes influences multiple aspects of sensorimotor circuit formation. More generally, they suggest that regional astrocyte heterogeneity may help to coordinate postnatal neural circuit refinement. 12 total samples consisting of three biological replicates each of flow sorted postnatal day 7 dorsal spinal cord astrocytes, ventral spinal cord astrocytes, dorsal SC non astrocytes, and ventral SC non astrocytes

2014-05-02 | E-GEOD-55054 | biostudies-arrayexpress

Rat Astrocyte-Neuron Co-cultures versus purified co-cultured Astrocytes versus Astrocyte alone

Project description:Profiling of transcriptional changes in rat astrocytes when co-cultured with neurons: comparison of astrocytes cultured alone with astrocytes co-cultured with mouse hippocampal neurons. Co-cultured astrocytes are isolated using cold jet, a novel tool for these neuron-glia cultures. Over the last decade, the importance of astrocyte-neuron communication in neuronal development and synaptic plasticity has become increasingly clear. Since neuron-astrocyte interactions represent highly dynamic and reciprocal processes, we hypothesized that at least part of the involved astrocyte genes may be regulated as a consequence of their interactions with maturing neurons. In order to identify such neuron-induced astrocyte genes in vitro, we tested the effectiveness of the ‘cold jet’, a new method for separation of neurons from co-cultured astrocytes. The cold jet method is performed under ice-cold conditions and avoids protease-mediated isolation of astrocytes or time-consuming centrifugation, yielding intact astrocyte mRNA with approximately 90% of neuronal RNA removed. Using this method, we executed genome-wide profiling in which RNA derived from astrocyte-only cultures was compared with astrocyte RNA derived from differentiating neuron-astrocyte co-cultures. Data analysis revealed changes in expression of a large number of mRNAs and biological processes, including novel findings. Thus, cold jet is an efficient method to separate astrocytes from neurons in co-culture, and in this study reveals that neurons induce robust gene-expression changes in co-cultured astrocytes.

2016-11-09 | GSE52481 | GEO

Transcriptional changes and microRNA expression profiles during NeuroD1-mediated astrocyte-to-neuron conversion

Project description:To reveal the molecular mechanisms underlying astrocyte-to-neuron reprogramming, we performed RNA-seq analysis on human astrocyte cultures (HA1800) during NeuroD1(ND1)-mediated neuronal reprogramming.

2023-07-10 | GSE214749 | GEO

Pyramidal neuron subtype diversity governs microglia states in the neocortex [MERFISH]

Project description:Pyramidal neuron subtype diversity governs microglia states in the neocortex [MERFISH]

| PRJNA797656 | ENA

Specification of a rostro-caudal axis in cortical assembloids through a polarized source of FGF8 (scRNA-Seq)

Project description:Current organoid protocols are widely used to mechanistically study cortical development, evolution and brain pathologies. While these systems generate all major cortical cell types in histologically distinct compartments, they lack cortical area topography, which is initiated by gradients of signaling molecules released by signaling organizers that establish transcriptionally distinct domains along the rostro-caudal axis of the developing cortex. Here, we engineer human cortical assembloids that combine an organizer-like structure expressing FGF8 with an elongated organoid design to enable the controlled modulation of FGF8 signaling along the longitudinal organoid axis. We demonstrate that individual polarized cortical assembloids (polCA) mount a position-dependent transcriptional program that matches the in vivo rostro-caudal gene expression patterns. Importantly, positional identity is lost in polCA carrying a mutation in the FGFR3 gene associated with temporal lobe malformations and intellectual disability in humans. Similar to in vivo, this program is accompanied by transcriptional divergence of radial glia cells and excitatory neurons and their segregation along the longitudinal axis of individual organoids. Thus, this method reproduces in vivo cortical topography in individual organoids and enables the analysis of area-related phenotypes underlying human disorders.

2024-05-03 | GSE231319 | 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