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Atlas of Brain-Permeable Blood Proteins Links Neuroprotection to Alzheimer's Risk Genes [bulk_RNAseq_astrocyte]

GSE301828 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/07/03 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 16 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
16 samples: 8 × Untreated astrocytes, vs 8 × APOA1 treated astrocytes,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.
Summary (written by the submitters)
The blood-brain barrier (BBB) is a highly selective interface that traditionally has been seen as restricting blood-borne substances from entering the brain. Despite its essential role in brain health and disease, the extent and functional impact of physiological blood-to-brain protein transport remain largely unexplored. Here, we use a combination of bioorthogonal chemistries, blood proteome labeling, and mass spectrometry to discover the repertoire of BBB-permeable proteins in healthy mice.
Read the full summary ↓
We discovered that the brain vasculature actively samples hundreds of diverse circulatory proteins under physiological conditions. Many of these proteins accumulate in the brain, showing distinct enrichment patterns across both functional protein classes and anatomical brain regions. In models of neuroinflammatory and neurodegenerative diseases, the composition of BBB-permeable proteins changed significantly, implicating dysregulated protein transport in disease pathogenesis. Notably, single-injection validation experiments revealed that BBB-permeable proteins exhibit cell type-specific targeting to neurons, astrocytes, or microglia, suggesting specialized functional roles. Focusing on apolipoprotein A1 (APOA1), we demonstrate its entry via brain endothelial SCARB1 receptor, its selective accumulation in astrocytes and its interaction with the ABCA1 receptor—a critical AD risk gene that also binds APOE, the strongest genetic risk factor for late-onset Alzheimer's disease. This peripheral-central interaction promotes cholesterol efflux in astrocytes and protects neuronal synapses from degeneration. Overall, our study redefines the BBB as a dynamic conduit for the transport of specific, neuroprotective circulatory proteins into the healthy brain and establishes a molecular link between peripheral factors and Alzheimer's risk genes.
This dataset
Open GSE301828 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 GSE301828_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1287620 and SRA study SRP598972. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 × Untreated astrocytes, vs 8 × APOA1 treated astrocytes,

Supports a between-group comparison across 16 samples.

How we read this: 2 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
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.