GEO series

Single-Cell Transcriptomic Analysis of Cellular Composition and Signaling Pathways in Cerebral Cavernous Malformation

GSE294555 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/04/15 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 12 samples: 3 × STA, epilepsi, # vs 3 × STA_BCR, epilepsi, # vs 3 × STA_TCR, epilepsi, #Groups 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: Single-cell transcriptome profiling reveals dynamic cell populations and immune infiltration in cerebral cavernous malformationFrontiers in immunology · 2025

Summary (written by the submitters)

Lesional brain vascular tissues from CCM patients and normal brain vascular tissues from healthy controls were collected. Multiplex fluorescent immunohistochemistry and single-cell RNA sequencing were performed on the lesional tissues. Differential gene expression, pathway enrichment analysis, and cell-cell communication analysis were conducted to investigate disease-related changes.

Read the full summary ↓

We identified 8 major cell types in the lesion tissues of CCM patients. We observed an increased proportion of monocytes, neutrophils, and NK cells in the lesion tissues of CCM patients. Twenty-eight significantly differentially expressed genes were identified, and pathways such as Natural Killer cell-mediated cytotoxicity showed alterations. Cell-cell communication analysis revealed an increase in both the types and strength of communication between cells in the CCM lesion tissues.

Published in

Single-cell transcriptome profiling reveals dynamic cell populations and immune infiltration in cerebral cavernous malformation

Han Z, Lei C, Zhou Z et al. · Frontiers in immunology 2025 · PMID 40519934 · doi:10.3389/fimmu.2025.1592343

This dataset

Open GSE294555 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 GSE294555_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 PRJNA1250490 and SRA study SRP578428. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40519934) ↗

Study design

3 × STA, epilepsi, # vs 3 × STA_BCR, epilepsi, # vs 3 × STA_TCR, epilepsi, #

Supports a between-group comparison across 9 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 9 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

GSM8910954 STA, epilepsi, #1 STA, epilepsi, #
GSM8910955 STA, epilepsi, #2 STA, epilepsi, #
GSM8910956 STA, epilepsi, #4 STA, epilepsi, #
GSM8910957 STA, CCM, #1
GSM8910958 STA_BCR, epilepsi, #1 STA_BCR, epilepsi, #
GSM8910959 STA_TCR, epilepsi, #1 STA_TCR, epilepsi, #
GSM8910960 STA_BCR, epilepsi, #2 STA_BCR, epilepsi, #
GSM8910961 STA_TCR, epilepsi, #2 STA_TCR, epilepsi, #
GSM8910962 STA_BCR, epilepsi, #4 STA_BCR, epilepsi, #
GSM8910963 STA_TCR, epilepsi, #4 STA_TCR, epilepsi, #
GSM8910964 STA,_BCR CCM, #1
GSM8910965 STA_TCR, CCM, #1

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