GEO series

Analysis of MDD and control patients by snRNA-seq

GSE262854 Homo sapiens (human) Single-nucleus RNA-seq 2 samples Submitted 2025/03/03 Platform GPL21697

At a glance

Single-nucleus RNA-seq · human · 2 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).
Organism: Homo sapiens (human)
Samples: 2 samples
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: Psychedelic control of neuroimmune interactions governing fearNature · 2025

Summary (written by the submitters)

Neuroimmune interactions—signals transmitted between immune and brain cells—regulate many aspects of tissue physiology including responses to psychological stress, which can predispose individuals to develop neuropsychiatric diseases. Still, the interactions between hematopoietic and brain-resident cells that influence complex behaviors are poorly understood.

Read the full summary ↓

Here, we used a combination of genomic and behavioral screens to demonstrate that astrocytes in the amygdala limit stress-induced fear behavior through EGFR. Mechanistically, amygdala astrocyte EGFR expression inhibits a stress-induced pro-inflammatory signal transduction cascade that facilitates neuro-glial cross-talk and stress-induced fear behavior through the orphan nuclear receptor NR2F2 in amygdala neurons. We uncovered that, in turn, decreased EGFR signaling and fear behavior were associated with meningeal monocyte recruitment during chronic stress. This set of neuroimmune interactions was therapeutically targetable by psychedelic administration, which reversed monocyte accumulation in the brain meninges along with fear behavior. Together with validation in clinical samples, these data suggest that psychedelics can be used to target neuroimmune interactions relevant to neuropsychiatric disorders and potentially other inflammatory diseases.

Published in

Psychedelic control of neuroimmune interactions governing fear

Chung EN, Lee J, Polonio CM et al. · Nature 2025 · PMID 40269152 · doi:10.1038/s41586-025-08880-9

This dataset

Open GSE262854 in finder → Find more human 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 GSE262854_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 PRJNA1093488 and SRA study SRP498763. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40269152) ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

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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.