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scRNA-seq analyses of cerebrospinal fluid (CSF) cells in older adults with or without Alzheimer's disease after Bacillus Calmette Guerin (BCG) vaccination.

GSE281606 Homo sapiens (human) Single-cell RNA-seq 34 samples Submitted 2026/04/27 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 34 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
34 samples: 34 samples, each with a distinct title — no replicated groupsGroups 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
Bacillus Calmette-Guérin (BCG) immunotherapy reprograms CNS immunity and alters Alzheimer's biomarkers: results from two open-label clinical trialsCommunications medicine · 2026
Summary (written by the submitters)
Cerebrospinal Fluid cells collected from older adults before and after BCG vaccination were studied. This database is part of the following. NCT04507126 - A Pilot Study of the Effects of Bacillus Calmette-Guérin (BCG) Immunization on Cerebrospinal Fluid and Blood-based Biomarkers in Older Adults - ClinicalTrials.gov. https://clinicaltrials.gov/ct2/show/NCT04507126 NCT05004688 - A Trial to Evaluate the Effects of BCG in Adults With MCI and Mild-to-Moderate AD - - ClinicalTrials.gov. https://clinicaltrials.gov/ct2/show/NCT05004688
Published in
Bacillus Calmette-Guérin (BCG) immunotherapy reprograms CNS immunity and alters Alzheimer's biomarkers: results from two open-label clinical trials
Weinberg MS, Kodali MC, Li Z et al. · Communications medicine 2026 · PMID 42393277 · doi:10.1038/s43856-026-01691-7
This dataset
Open GSE281606 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 GSE281606_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 PRJNA1184787 and SRA study SRP544513. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42393277) ↗
Study design
34 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 34 sample titles: 34 distinct titles with little repetition. 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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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.