GEO series

Comparative Single Cell Transcriptome Analysis of c-Met Receptor Expressing and Non-Expressing Projection Neurons in the Developing Frontal and Visual Cortices

GSE276009 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/09/30 Platform GPL34328

At a glance

Single-cell RNA-seq · mouse · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 12 samples: 7 × Frontal cortex, P7-P9, vs 5 × Visual cortex, P7-P9,Groups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Comparative Single-Cell Transcriptome Analysis of c-Met Receptor Expressing and Non-Expressing Projection Neurons in the Developing Frontal and Visual CorticesDevelopmental neuroscience · 2025

Summary (written by the submitters)

Single cell transcriptomic analyses in adult mice show that cortical projection neuron (PN) subclasses exhibit heterogenous gene expression profiles that reflect their projection targets, and laminar and areal positions. Further analyses revealed that PNs within the same subclass also exhibit transcriptomic heterogeneity. The MET receptor tyrosine kinase, a regulator of synapse maturation, is expressed in a subpopulation of select cortical PN subclasses, providing an experimental model to address transcriptomic heterogeneity within PN subclasses.

Read the full summary ↓

Single cell RNA sequencing and smFISH identified transcriptomic differences between Met+ and Met- PN populations in the mouse visual and frontal cortices during the early phase of synapse formation and dendritic growth. Analyses confirmed enrichment of Met in select PN subclasses and further identified astrocytes as the major source of its ligand, Hgf. No genes were expressed uniquely in Met+ or Met- PNs within a subclass; rather, there were graded differences in gene expression between the populations. While the identity of differentially expressed genes varied between subclass and cortical area, there was a consistent overrepresentation of genes associated with axon growth, and synapse structure, development and function, with a subset associated with the MET interactome. Further, expression differences in genes associated with maturation indicate less mature excitatory synapses and spines in the Met+ population at this age. These findings suggest that Met+ neurons do not represent a functional subtype within a PN subclass. Rather, the data are consistent with converging lines of biochemical and electrophysiological evidence that MET contributes to asynchronous maturation of developing cortical circuits.

Published in

Comparative Single-Cell Transcriptome Analysis of c-Met Receptor Expressing and Non-Expressing Projection Neurons in the Developing Frontal and Visual Cortices

Ali Marandi Ghoddousi R, Levitt P, Rady Z et al. · Developmental neuroscience 2025 · PMID 40996948 · doi:10.1159/000548617

This dataset

Open GSE276009 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE276009_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1154267 and SRA study SRP529466. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40996948) ↗

Study design

7 × Frontal cortex, P7-P9, vs 5 × Visual cortex, P7-P9,

Supports a between-group comparison across 12 samples.

How we read this: 2 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8489340 Frontal cortex, P7-P9, replicate 1 Frontal cortex, P7-P9,
GSM8489341 Frontal cortex, P7-P9, replicate 2 Frontal cortex, P7-P9,
GSM8489342 Frontal cortex, P7-P9, replicate 3 Frontal cortex, P7-P9,
GSM8489343 Frontal cortex, P7-P9, replicate 4 Frontal cortex, P7-P9,
GSM8489344 Frontal cortex, P7-P9, replicate 5 Frontal cortex, P7-P9,
GSM8489345 Frontal cortex, P7-P9, replicate 6 Frontal cortex, P7-P9,
GSM8489346 Frontal cortex, P7-P9, replicate 7 Frontal cortex, P7-P9,
GSM8489347 Visual cortex, P7-P9, replicate 1 Visual cortex, P7-P9,
GSM8489348 Visual cortex, P7-P9, replicate 2 Visual cortex, P7-P9,
GSM8489349 Visual cortex, P7-P9, replicate 3 Visual cortex, P7-P9,
GSM8489350 Visual cortex, P7-P9, replicate 4 Visual cortex, P7-P9,
GSM8489351 Visual cortex, P7-P9, replicate 5 Visual cortex, P7-P9,

Datasets on a similar topic

GSE275643 Single cell RNA-seq reveals GINIP-Expressing neurons as the main targets of focused ultrasoud. 57 samples shares expressing, neurons
GSE266395 Acetaminophen overdose reveals protease activated receptor 4 as a low expressing but potent receptor on the hepatic endothelium in mice 48 samples shares expressing, receptor
GSE243169 Lung-innervating neurons expressing TMC3 control broncho-constriction and dilation with direct impact on lung tidal volume 38 samples shares expressing, neurons
GSE232496 Lung-innervating neurons expressing TMC3 control broncho-constriction and dilation with direct impact on lung tidal volume (RNA-Seq) 30 samples shares expressing, neurons
GSE284096 Targeted Apoptosis of the Angiotensin AT1R (Agtr1a)-Expressing Subtype of Agouti-Related Peptide Neurons in Adult Mice Increases Food Intake and Resting Metabolism, and Alters Blood Pressure Control 24 samples shares expressing, neurons
GSE281444 Definitive Evidence for the Identification and Function of Renin-Expressing Cholinergic Neurons in the Nucleus Ambiguus 21 samples shares expressing, neurons
GSE316516 Projection-defined amygdala neurons encode emotional memory through distinct transcriptomic programs 15 samples shares projection, neurons
GSE296646 Comparative single-cell analysis of multiple models of retinitis pigmentosa reveals common pro-survival mechanisms activated in photoreceptors 13 samples shares comparative, receptor

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.