Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MERFISH spatial transcriptomic profiling of Sst+ interneurons in the postnatal mouse brain

ABSTRACT: Spatially resolved transcriptomic profiling of somatostatin-positive (Sst+) interneurons in the postnatal mouse brain using MERFISH (MERSCOPE, Vizgen). Two coronal brain sections corresponding to Paxinos Atlas levels 125 and 133 were collected from P5 C57BL/6J mice to characterize Sst+ cell type diversity and spatial organization

ORGANISM(S): Mus musculus synthetic construct

PROVIDER: GSE330849 | GEO | 2026/05/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

MERFISH analysis of Sst-Cre mediated Dnmt1 knockout at E16.5

Project description:To investigate the effects of Dnmt1 Knockout in Sst expressing interneurons on celltype distribution in the embryonic brain, Sst-Cre/tdTomato/Dnmt1 loxp2 knockout mice and Sst-Cre/tdTomato control mice were analysed. 10 µm coronal sections of E16.5 brains were prepared for the Merscope platform using the commercially available Pan Neuro panel (Vizgen), covering 500 distinct transcripts.

2025-06-18 | GSE298591 | GEO

MERFISH analysis of Sst-Cre mediated Dnmt1 knockout at E16.5

Project description:MERFISH analysis of Sst-Cre mediated Dnmt1 knockout at E16.5

| PRJNA1269984 | ENA

Spatial transcriptomics of P35 septum

Project description: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

2025-04-13 | GSE282127 | GEO

MEF2C CUT&RUN in PV and SST interneurons.

Project description:CUT&RUN for MEF2C in mature PV+ and SST+ cortical interneurons to characterize the differential usage of this transcription factor by these populations.

2021-09-22 | GSE165018 | GEO

MEF2C CUT&RUN in PV and SST interneurons.

Project description:MEF2C CUT&RUN in PV and SST interneurons.

| PRJNA692975 | ENA

Macrophage signaling associates with fibrogenic program activation in periductal fibroblasts in pediatric primary sclerosing cholangitis.

Project description:Two diagnostic liver biopsy specimens from pediatric patients with primary sclerosing cholangitis were profiled by single-cell spatial transcriptomics using the VizGen MERSCOPE platform with a custom 400-gene liver immunology panel. The material consisted of freshly cut, unstained sections from archived FFPE needle biopsies mounted on VizGen-provided slides for hybridization according to the manufacturer’s protocol. Both specimens contained focal periductal and bridging fibrosis.

2026-04-15 | GSE325861 | GEO

m1A methylase TRMT6 promotes neuroblastoma development by demethylating SST mRNA in an m1A/YTHDF2-dependent manner

Project description:m1A, a prevalent RNA modification found in various RNA species, was recently reported to modulate cancer progression; However its effects in neuroblastoma have not been investigated. In this study, we observed a significantly elevated expression of m1A transmethylase TRMT6 in high-risk and late-stage neuroblastoma patients. Silence and regain of function studies demonstrated that TRMT6 promotes neuroblastoma cell malignancy, tumor growth, and metastasis in vitro and in vivo. Omics analysis and cancer malignancy assay revealed that somatostatin (SST) is the functional downstream target of TRMT6, which determined the pro-tumor role of TRMT6 in neuroblastoma. Mechanistically, TRMT6 reduces SST mRNA levels by inhibiting its mRNA stability in an m1A-YTHDF2-dependent manner, which revealed the crosstalk of the m1A methylase TRMT6 in neuroblastoma. Moreover, SST analog octreotide suppresses neuroblastoma cell malignancy, tumor growth, and metastasis. Targeting TRMT6 provides a novel potential diagnosis and therapeutic target for neuroblastoma

2025-12-01 | GSE297545 | GEO

Three-dimensional Co-culturing Reveals Human Stem Cell-Derived Somatostatin Interneurons with Subclass Expression

Project description:Cortical interneuron deficiencies, particularly involving the somatostatin (SST) subtypes, contribute to neurological and neuropsychiatric disorders. These interneurons are difficult to derive in vitro from human embryonic stem cells (hESCs) due to their late embryonic development and dependence on glial interaction. To this end, we developed a three-dimensional co-culture model of hESC-derived neurons, enabling long-term development, functional maturity, and neuron-glial interaction. Under these conditions, hESCs successfully differentiated into functional GABAergic interneurons expressing the SST gene and protein within 50 days. Single-nuclei RNA sequencing revealed transcripts for SST subclasses, including Martinotti, non-Martinotti, and long-projecting neurons, that have not yet been described for hESC cultures. Upon injection into forebrain organoids, the interneuron progenitors spread and functionally matured while retaining their SST subclass identities, suggesting cell-intrinsic fate specification. Our in vitro model provides a robust platform for studying human SST interneurons, offering new avenues for investigating their role in health and disease.

2025-09-09 | GSE305121 | GEO

Transcriptional alterations in Nucleus Accumbens somatostatin interneurons following exposure to cocaine

Project description:Total RNA-sequencing of FACs isolated nucleus accumbens somatostatin interneuron nuclei Somatostatin interneuron loss in multiple cortical brain regions has been observed postmortem in humans with several neuropsychiatric disorders and their loss is proposed to underlie some common pathological changes in circuit function across numerous syndromes. However, somatostatin interneurons in the nucleus accumbens (NAc), a key brain reward region, remain poorly understood due to the fact that these cells account for <1% of NAc neurons. Here, we used Flouresence activated cell sorting to isolate nuclei of somatostatin-expressing interneurons in the Nucleus Accumbens from individual SST-TLG498 reporter mice that express membrane bound EGFP-F specifically in somatostatin-expressing neurons. We then performed cell-type specific Total RNA-sequencing to characterize the entire transcriptome of NAc somatostatin interneurons after repeated exposure (7 days) to either saline or cocaine. We identified a wide variety of coding and non-coding transcripts that were expressed at high levels and were differentially expressed between saline and cocaine treated mice. Repeated cocaine administration induces transcriptome-wide changes in gene expression within NAc somatostatin interneurons, with particular regulation of transcripts related to neural plasticity. Our results identify alterations in NAc induced by cocaine in a sparse population of somatostatin interneurons, and illustrate the value of studying brain diseases using cell type-specific whole transcriptome RNA-sequencing to identify novel neurpathophysiology.

2018-07-03 | GSE116484 | GEO

Molecular Cartography of the Human and Mouse Down Syndrome Brain [MERFISH]

Project description:Given the importance of linking human and model system pathobiology, we also performed highly multiplexed RNA in situ spatial transcriptomics on a well-established trisomic mouse model (Ts65Dn) to study the cellular landscape of the trisomic brain during early life and aging. We profiled the spatial transcriptome of > 240,000 cells in the mouse brain and identified trisomy-associated gene expression patterns in the molecular control of neurogenesis, gliogenesis, and myelination. Multiplexed error-robust fluorescence in situ hybridization (MERFISH) was performed on postnatal day 0 (P0) and 6 month (6mo) euploid and trisomic (Ts65Dn) mice (n=3 per condition). Coronal sections of the entire brain were used for analysis.

2025-07-11 | GSE280177 | 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