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Multimodal perspectives on the upper layer neurogenesis in the murine cerebral cortex

GSE248250 Mus musculus (mouse) RNA-seq (gene expression) 137 samples Submitted 2026/07/31 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 137 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
137 samples: 24 conditions, mostly with about 6 replicates eachGroups 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.
Summary (written by the submitters)
Upper layer corticogenesis provides mammals with a range of additional cognitive circuits. Through indirect neurogenesis, neuronal progenitor cells transition from radial glia cells to an intermediate stage, where they exponentially increase neuronal output, migrate into the upper regions of the neocortex, and settle as excitatory projection neurons.
Read the full summary ↓
During this process, Glast1+ (Glutamate aspartate transporter 1) progenitor cells exit the cell cycle, begin to express NeuroD1 (Neuronal Differentiation 1), and irreversibly commit to a neuronal fate. The regulatory landscape governing the specific formation of the upper layers is not fully understood. In particular, the molecular mechanisms underlying the gradual transition of neurons into the post-mitotic state remain unresolved. A central question in this process is the influence of prenatal stressors on upper layer corticogenesis. In this study, we created a multimodal map of neurogenesis under both untreated and immune-activated conditions in a mouse model. Thereby, we monitored subtle canonical Wnt pathway-associated patterns that could explain the spontaneous aetiology of autism spectrum disorders or late-onset neurodegenerative diseases.
This dataset
Open GSE248250 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 GSE248250_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1043106 and SRA study SRP473033. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
24 conditions, mostly with about 6 replicates each
C treatment, ×20 E14, mixed brain cell population, w/o treatme… ×6 E14, pGlast cell population, w/o treatment, ×6 E16, mixed brain cell population, w/o treatme… ×6 E16, pNeuroD cell population, w/o treatment, ×6 E17, mixed brain cell population, w/o treatme… ×6 E17, pNeuroD cell population, w/o treatment, ×6 E18, mixed brain cell population, w/o treatme… ×6 +21 more

Supports a between-group comparison across 132 samples.

How we read this: 24 replicated groups read from 137 sample titles; they account for 132 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

+ 97 more — browse all 137 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.