GEO series

Single Cell Transcriptional Signatures of Microglia and Monocytes after ICH

GSE333172 Homo sapiens (human) Single-cell RNA-seq 20 samples Submitted 2026/08/12 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 20 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: 20 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.

Summary (written by the submitters)

CNS-resident microglia and recruited myeloid cells populate the haematoma in intracerebral haemorrhage (ICH), but the contribution of these cell populations to injury and repair has been controversial. To better characterise myeloid cell changes over time, we employed single-cell RNA sequencing to generate a unique paired dataset of live haematoma and peripheral blood samples from 10 ICH patients.

Read the full summary ↓

This work presents a temporal atlas of ICH myeloid populations and identifies population-specific in-situ transcriptional drivers. In addition to distinct populations of activated microglia and TNF-low microglia, we found a unique and highly activated population of CD14+ monocytes in the haematoma. Perturbation analysis comparing haematoma-associated monocytes to shared populations in blood and haematomas identified TNF signalling as the primary driver of their activation. Employing a custom temporal trajectory analysis based on the embeddings of a single-cell foundation model, we found that this TNF response in monocytes was transient, peaking early after haemorrhage and decreasing over the ensuing 48 hours. Our analysis further identified a transient population of highly activated microglia as the likely source of TNF during the acute stage of ICH. Acute TNF signalling in CD14+ monocytes associated with better adjusted outcomes both in our and external cohorts. Overall, our results suggest that acute TNF signalling between transient populations of activated microglia and unique haematoma-associated monocytes could potentially be beneficial in recovery after ICH.

This dataset

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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 GSE333172_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 PRJNA1470264 and SRA study SRP703483. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42454753) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 20 more — browse all 20 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.