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Sex-Biased Transcription in Early Postnatal Layer 2/3 Cortical Neurons: Interplay Between Sex and Cux1/2 Mutations

GSE310138 Mus musculus (mouse) RNA-seq (gene expression) 43 samples Submitted 2026/05/20 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 43 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
43 samples: 13 conditions, mostly with about 4 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.
Paper
A transient sex-biased transcriptional program shapes early postnatal L2/3 neuron developmentBiology of sex differences · 2026
Summary (written by the submitters)
Despite many neurodevelopmental disorders (NDDs) exhibiting pronounced sex differences, the role of sex in shaping the genetic regulation of the brain remains barely explored. Brain development relies on a precise control of gene expression across time and disruptions in this process, especially during critical periods, can result in NDDs.
Read the full summary ↓
In the neocortex, layer (L) 2/3 excitatory pyramidal neurons stand out for integrating information across cortical areas and hemispheres. Here, we show a transient window of sex-biased gene expression of L2/3 neurons at postnatal day 4 (P4), mainly characterized by autosomal genes. Loss-of-function experiments targeting Cux1 and Cux2, key transcription factors in L2/3 development, lead to sex-dependent transcriptional deregulation in these neurons, with a significant male-biased sensitivity. Moreover, differentially expressed genes shift substantially between developmental stages, reflecting the dynamic regulation of Cux-mediated gene expression. Overall, our study identifies P4 as a key determinant of early sex differences and highly vulnerable stage for the emergence of NDDs, and highlights the importance of sex-specific analyses for understanding brain development and disease.
Published in
A transient sex-biased transcriptional program shapes early postnatal L2/3 neuron development
Marcos-Grañeda E, Martín-Fernández F, Weiss LA et al. · Biology of sex differences 2026 · PMID 41952201 · doi:10.1186/s13293-026-00885-x
This dataset
Open GSE310138 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 GSE310138_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 PRJNA1365189 and SRA study SRP645155. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41952201) ↗
Study design
13 conditions, mostly with about 4 replicates each
L2/3 neurons, Cux1 KO, E19, Female ×4 L2/3 neurons, Cux1 KO, E19, Male ×4 L2/3 neurons, Cux2 KO, E19, Female ×4 L2/3 neurons, Cux2 KO, E19, Male ×4 L2/3 neurons, WT, E19, Female ×4 L2/3 neurons, WT, E19, Male ×4 L2/3 neurons, WT, P4, Female ×3 L2/3 neurons, WT, P4, Male ×3 +5 more

Supports a between-group comparison across 43 samples.

How we read this: 13 replicated groups read from 43 sample titles; they account for 43 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

+ 3 more — browse all 43 samples with per-sample file links →

Datasets on a similar topic

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