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Blood RNA transcripts show changes in inflammation and lipid metabolism in Alzheimer’s disease and mitochondrial function in mild cognitive impairment

GSE249477 Homo sapiens (human) RNA-seq (gene expression) 62 samples Submitted 2025/03/05 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 62 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
Homo sapiens (human)
Samples
62 samples: 62 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
Blood RNA transcripts show changes in inflammation and lipid metabolism in Alzheimer's disease and mitochondrial function in mild cognitive impairmentJournal of Alzheimer's disease reports · 2024
Summary (written by the submitters)
Abnormal immunity in the periphery appears to be involved in the pathogenesis of Alzheimer’s disease (AD). In this study, blood transcriptome analyses of patients with AD, those with mild cognitive impairment (MCI) due to AD, and heathy controls were performed to elucidate immune-mediated pathophysiology. The sample included 63 subjects from the Nakayama Study who were clinically diagnosed as (1) healthy controls (N=21), (2) having MCI due to AD (N=20), and (3) having AD (N=21).
Read the full summary ↓
Blood samples were taken, magnetic resonance imaging was performed, and questionnaires were administered. RNA-seq, differential gene expression, gene ontology, pathway enrichment, and ingenuity pathway analyses were conducted, and polymerase chain reaction testing was performed. The results showed that neutrophil extracellular trap signaling was increased, and lipid metabolism (FXR/RXR activation, triacylglycerol degradation) was decreased in AD, whereas MCI showed protective responses via decreased neutrophil extracellular trap signaling and mitochondrial functions such as upregulation of the sirtuin pathway and downregulation of oxidative stress. Based on these findings, immune cells appear to have important roles in the pathogenesis of AD, and the transcriptome in blood may be useful as a biomarker for diagnosis via monitoring immunity in MCI and AD.
Published in
Blood RNA transcripts show changes in inflammation and lipid metabolism in Alzheimer's disease and mitochondrial function in mild cognitive impairment
Iga JI, Yoshino Y, Ozaki T et al. · Journal of Alzheimer's disease reports 2024 · PMID 40034360 · doi:10.1177/25424823241307878
This dataset
Open GSE249477 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 GSE249477_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 PRJNA1049359 and SRA study SRP476140. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40034360) ↗
Study design
62 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 41 samples read as cases, 21 as controls.

How we read this: Read from 62 sample titles: 62 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

+ 22 more — browse all 62 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.