Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cosmx Spatial Analysis of whole brain slices and ventral pallidum

ABSTRACT: Pilot Cosmx experiment to explore and spatially atlas cell types present in the Striatum

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE292791 | GEO | 2025/03/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Cosmx Spatial Analysis of whole brain slices and ventral pallidum

Project description:Cosmx Spatial Analysis of whole brain slices and ventral pallidum

| PRJNA1241259 | ENA

Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer [CosMx]

Project description:Patients with treatment-refractory pancreatic cancer often succumb to widespread systemic metastases; however, the transcriptomic heterogeneity that underlies recalcitrance to therapy remains understudied, particularly in the spatial context. We constructed high-resolution spatial maps of transcriptional heterogeneity, clonal architecture and lineage plasticity using spatially resolved transcriptomics (SRT) from 13 primary cancers and 36 corresponding liver, lung, and peritoneal metastases, collected via a rapid (“warm”) autopsy program. To validate findings from our SRT dataset at single-cell resolution, we performed CosMX SMI profiling (Nanostring) on 7 samples from 3 patients, including primary and/or liver metastasis.

2025-02-21 | GSE277782 | GEO

IBD CosMx NanoString data from colonic mucosa

Project description:Inflammatory bowel diseases (IBDs) including ulcerative colitis (UC) and Crohn’s disease (CD) are chronic inflammatory diseases with increasing worldwide prevalence that show a perplexing heterogeneity in manifestations and response to treatment. We applied spatial transcriptomics at single-cell resolution (CosMx Spatial Molecular Imaging) to human inflamed and uninflamed intestine.

2023-06-13 | GSE234713 | GEO

Transcriptomic landscape of mammalian ventral pallidum at single-cell resolution

Project description:The ventral pallidum (VP) is critical for motivated behaviors. While contemporary work has begun to elucidate the functional diversity of VP neurons, the molecular heterogeneity underlying this functional diversity remains incompletely understood. We used snRNA-seq and in situ hybridization to define the transcriptional taxonomy of VP cell types in mice, macaques, and baboons. We found transcriptional conservation between all three species, within the broader neurochemical cell types. Unique dopaminoceptive and cholinergic subclusters were identified and conserved across both primate species but had no homolog in mice. This harmonized consensus VP cellular atlas will pave the way for understanding the structure and function of the VP and identified key neuropeptides, neurotransmitters, and neuro receptors that could be targeted within specific VP cell types for functional investigations.

2024-10-30 | GSE277465 | GEO

GeoMX spatial transcriptomic on biphasic Malignant Pleural Mesothelioma

Project description:We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morpho-logical evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler and Cancer Transcriptome Atlas to compare epithelioid and sarcomatoid components transcriptional profile and reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions.

2023-12-07 | E-MTAB-13043 | biostudies-arrayexpress

IBD CosMx NanoString data from colonic mucosa

Project description:IBD CosMx NanoString data from colonic mucosa

| PRJNA982807 | ENA

Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer [CosMx]

Project description:Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer [CosMx]

| PRJNA1164180 | ENA

Ventral pallidum neurons dynamically signal relative threat.

Project description:The ventral pallidum (VP) is anatomically poised to contribute to threat behavior. Recent studies report a VP population that scales firing increases to reward but decreases firing to aversive cues. Here, we tested whether firing decreases in VP neurons serve as a neural signal for relative threat. Single-unit activity was recorded while male rats discriminated cues predicting unique foot shock probabilities. Rats' behavior and VP single-unit firing discriminated danger, uncertainty, and safety cues. Two populations of VP neurons dynamically signaled relative threat, decreasing firing according to foot shock probability during early cue presentation, but disproportionately decreasing firing to uncertain threat as foot shock drew near. One relative threat population increased firing to reward, consistent with a bi-directional signal for general value. The second population was unresponsive to reward, revealing a specific signal for relative threat. The results reinforce anatomy to reveal the VP as a neural source of a dynamic, relative threat signal.

| S-EPMC7794503 | biostudies-literature

Microglia - astrocyte cross-talk in the amyloid plaque niche of an Alzheimer’s disease mouse model as revealed by spatial transcriptomics (CosMx)

Project description:In this study, we characterize the transcriptomic alterations, cellular compositions, and signaling perturbations in the amyloid plaque niche in an AD mouse model using high-resolution spatial transcriptomics (CosMx and Stereo-seq). We discover a wide heterogeneity in the cellular composition of amyloid plaque niches, marked by an increase in microglial accumulation over time. We profile the alterations of glial cells as they are exposed to plaques, and conclude that the microglial response to plaques is consistent across different brain regions, while the astrocytic response is more heterogeneous. In turn, as the microglial density of plaque niches increases, astrocytes acquire a more neurotoxic phenotype and play a key role in inducing GABAergic signaling and decreasing glutamatergic signaling in neurons of the hippocampus. Taken together, we show that astrocytic signaling around plaque pathology is disrupted with increasing microglial density, which in turn induces an imbalance in synaptic signaling in neurons in the hippocampus.

2024-04-19 | GSE263791 | GEO

Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identified that loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition

Project description:We used spatially resolved transcriptomics to define the cellular diversity within a sonic hedgehog (SHH) patient-derived model of Medulloblastoma (MB) and identify how cells specific to a transcriptional state or spatial location are pivotal in responses to treatment with the CDK4/6 inhibitor, Palbociclib. Our analysis reveals that SHH tumour in the mouse brain contains multiple malignant transcriptional states, recapitulating the extent of intratumoural cellular diversity identified in primary human SHH MB. Our study offers new insight into the previously described features of CDK4/6 inhibition in MB, with Palbociclib treatment inducing neuronal differentiation across all remaining cell types comprising the bulk of the SHH patient-derived orthotropic xenograft model. This study is, to the best of our knowledge, the first spatially resolved gene expression atlas of SHH PDOX MB and acts as proof-of-principle for the use of ST-seq in identifying spatially-organised tumour heterogeneity of MB.

2022-06-16 | E-MTAB-11720 | 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