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Single-nuleus RNA-sequencing of septal cells during postnatal development

GSE281738 Mus musculus (mouse) Single-nucleus RNA-seq 24 samples Submitted 2025/04/13 Platform GPL24247
At a glance

Single-nucleus RNA-seq · mouse · 24 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
24 samples: 10 conditions, mostly in duplicateGroups 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
Astrocyte specification in the mouse septum is shaped by both developmental origin and local signalsNature neuroscience · 2025
Summary (written by the submitters)
Purpose: The goal of this study is to use snRNA-seq to identify the diversity of cell types derived from Nkx2.1 lineage and non-Nkx2.1 lineages in the postnatal developing septum, and examine the cell trajectories, especially glial cells in the develping septum; Methods: The septum of P0, P3, P7,P14,P21 Nkx2.1Cre;SunGFP were collected, and nuclei of the septum cells were isolated, then GFP+ and GFP- nuclei were sorted out and followed by 10X genomics sequencing; Results: we
Read the full summary ↓
found diversity of astrocytes in the septum based on unique molecular profiles which follows the lineage separation, and we also observed the distinct developmental trajectories of subpopulation of astrocytes.
Published in
Astrocyte specification in the mouse septum is shaped by both developmental origin and local signals
Xie Y, Reid CM, Turrero Garcίa M et al. · Nature neuroscience 2025 · PMID 40721676 · doi:10.1038/s41593-025-02007-z
This dataset
Open GSE281738 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 GSE281738_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 PRJNA1185620 and SRA study SRP544907. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40721676) ↗
Study design
10 conditions, mostly in duplicate
Nkx_septum_P21_pos ×4 Nkx_septum_P21_neg ×4 Nkx_septum_P0_pos ×2 Nkx_septum_P0_neg ×2 Nkx_septum_P3_pos ×2 Nkx_septum_P3_neg ×2 Nkx_septum_P7_pos ×2 Nkx_septum_P7_neg ×2 +2 more

Supports a between-group comparison across 24 samples.

How we read this: 10 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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