GEO series

CD4+ T cells in the developing human brain shape angiogenesis and neurogenesis

GSE300932 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2026/06/26 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 16 samples: 8 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.

Summary (written by the submitters)

Although entry is limited, immune cells reside within and influence neural tissue function in health and disease. Unique T cell populations throughout the body may shape organogenesis, but these cells are absent during mouse embryogenesis. To investigate human prenatal T cell roles, we captured T cells from four midgestation organs: spleen, mesenteric lymph node, small intestine, and brain.

Read the full summary ↓

Single-cell RNA sequencing identified dominant CD4 populations and smaller subsets of cytotoxic CD8 and innate T cells. In the brain, distinct expression profiles were revealed, including a unique Trav1-2+ MAIT-like population. Spatial mapping showed T cells are predominantly localized within the ventricular angiogenic-neurogenic niche, adjacent to microglia. Functionally, co-culture of CD4 T cells and endothelial cells enhanced vascular network maturity, while transplanted CD4 T cells in brain organoids localized to the VZ niche and reduced cell death. Rag2 knock-out mice also show changes in brain vasculature and neuronal structure in the absence of B and T cells. These findings suggest T cells support tissue health and growth in the developing human brain and have implications for neurodevelopment in a growing population of surviving patients with immunodeficiency syndromes.

This dataset

Open GSE300932 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 GSE300932_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 PRJNA1260576 and SRA study SRP594932. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in duplicate

Brain GEX ×2 Brain TC ×2 MLN GEX ×2 MLN TC ×2 Small Intestine GEX ×2 Small Intestine TC ×2 Spleen GEX ×2 Spleen TC ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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

GSM9072393 Brain GEX 0588 Brain GEX
GSM9072394 Brain TCR 0588 Brain TC
GSM9072395 MLN GEX 0588 MLN GEX
GSM9072396 MLN TCR 0588 MLN TC
GSM9072397 Small Intestine GEX 0588 Small Intestine GEX
GSM9072398 Small Intestine TCR 0588 Small Intestine TC
GSM9072399 Spleen GEX 0588 Spleen GEX
GSM9072400 Spleen TCR 0588 Spleen TC
GSM9072401 Brain GEX 0723 Brain GEX
GSM9072402 Brain TCR 0723 Brain TC
GSM9072403 MLN GEX 0723 MLN GEX
GSM9072404 MLN TCR 0723 MLN TC
GSM9072405 Small Intestine GEX 0723 Small Intestine GEX
GSM9072406 Small Intestine TCR 0723 Small Intestine TC
GSM9072407 Spleen GEX 0723 Spleen GEX
GSM9072408 Spleen TCR 0723 Spleen TC

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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.