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Bone marrow myelopoiesis dysfunction in Alzheimer’s disease

GSE329430 Mus musculus (mouse) Single-cell RNA-seq 20 samples Submitted 2026/05/06 Platform GPL34328Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 20 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
Mus musculus (mouse)
Samples
20 samples: 6 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)
We have utilized single-cell RNA sequencing to analyze how Alzheimer's disease mouse model is affecting the bone marrow hematopoiesis at the single-cell level. We sorted and analyzed the myeloid cells and the hematopoietic stem and progenitor cells from the bone marrow and myeloid cell from the brains of WT and 5xFAD mice. We also analyzed sorted myeloid cells from 5xFAD chimeric mice that had received a bone marrow transplant from WT or IFNAR1-KO donors.
This dataset
Open GSE329430 in finder → Find more mouse 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 GSE329430_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 PRJNA1459226 and SRA study SRP695880. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in duplicate
bulk RNAseq. BM Monocytes from poly-IC-treate… ×4 bulk RNAseq. BM Monocytes from PBS-treated mi… ×3 Gene Expression. HSPC from WT and 5xFAD skull… ×2 CMO. HSPC from WT and 5xFAD skull and femur B… ×2 Gene Expression. Myeloid cells and HSPC from … ×2 HTO. Myeloid cells and HSPC from WT and 5xFAD… ×2 Gene Expression. Myeloid cells from WT and 5x… ×1 Gene Expression. Myeloid cells from WT_5xFAD … ×1 +3 more

Supports a case/control comparison: 7 samples read as cases, 13 as controls.

How we read this: 6 replicated groups read from 20 sample titles; they account for 15 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
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.