Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial Transcriptomics correlated Electron Microscopy [MERFISH]

ABSTRACT: Spatial Transcriptomics correlated Electron Microscopy [MERFISH]

PROVIDER: PRJNA836863 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Spatial Transcriptomics correlated Electron Microscopy

Project description:Spatial Transcriptomics correlated Electron Microscopy

| PRJNA836860 | ENA

Spatial Transcriptomics correlated Electron Microscopy [MERFISH]

Project description:Current spatial transcriptomics methods provide molecular and spatial information but no morphological readout. Here, we present STEM - a method that correlates multiplexed error-robust FISH with electron microscopy from neighboring tissue sections of the same sample. STEM links transcriptional and spatial organization of single cells with ultrastructural morphology of the tissue in vivo. Using STEM to characterize demyelinated white-matter lesions allowed us to link morphology of myelin-laden foamy microglia to transcriptional signature. Moreover, we revealed that interferon-response microglia have unique morphology and are enriched near CD8 T-cells.

2023-06-21 | GSE202623 | GEO

Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]

Project description:Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]

| PRJNA836864 | ENA

Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]

Project description:Current spatial transcriptomics methods identify cell types and states in a spatial context but lack morphological information. Electron microscopy, in contrast, provides structural details at nanometer resolution without decoding the diverse cellular states and identity. STEM address this limitation by correlating multiplexed error-robust FISH with electron microscopy from adjacent tissue sections. Using STEM to characterize demyelinated lesions in mice, we were able to bridge spatially resolved transcriptional data with morphological information on cell identities. This approach allowed us to link the morphology of foamy microglia and interferon-response microglia with their transcriptional signatures.

2023-06-21 | GSE202636 | GEO

Spatial Transcriptomics correlated Electron Microscopy

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-06-21 | GSE202638 | GEO

Primary ciliary dyskinesia without obvious electron microscopy defects

Project description:Primary ciliary dyskinesia without obvious electron microscopy defects

| PRJNA635175 | ENA

Primary ciliary dyskinesia without obvious electron microscopy defects

Project description:Primary ciliary dyskinesia without obvious electron microscopy defects

| PRJNA635176 | ENA

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

Project description: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

2026-05-26 | GSE330849 | GEO

MERFISH spatial transcriptomic profiling of extracellular matrix and vascular-associated populations in the adult human pancreas

Project description:The extracellular matrix (ECM) and basement membrane (BM) are critical structural and signaling components of the human pancreatic endocrine niche. To define the cellular sources and spatial organization of vascular ECM programs in the adult human pancreas, we performed MERFISH spatial transcriptomics on FFPE pancreatic tissue sections from non-diabetic (ND) and type 2 diabetic (T2D) donors using the Vizgen MERSCOPE platform with a custom 300-gene panel enriched for extracellular matrix, vascular, endocrine, and stromal-associated genes.

2026-06-02 | GSE333737 | GEO

MERFISH profiling of mouse retinal ganglion cell layer on wholemount

Project description:We optimized a workflow combining imaging-based spatial transcriptomics (MERFISH) and immunostaining on ganglion cell layer retinal flatmounts of C57/Bl6J mice.The MERFISH data shows molecularly-defined retinal ganglion cell types types exhibited non-uniform distributions. We also analyzed local neighborhoods for each cell and registered several RGC types as enriched in the perivascular niche.

2025-07-23 | GSE303399 | 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