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Frontal cortex pyramidal neuron expression profiles differentiate the prodromal stage from progressive degeneration across the Alzheimer’s disease spectrum

GSE285831 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2025/07/25 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 20 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
20 samples: 20 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.
Summary (written by the submitters)
Alzheimer's disease (AD) is an irreversible, progressive neurodegenerative disorder affecting an estimated 6.9 million Americans. There is no current treatment to prevent the onset or progression of dementia. Therefore, it is imperative to identify molecular and cellular mechanism(s) underlying the pathobiology of AD onset and progression.
Read the full summary ↓
We employed laser capture microdissection (LCM) to isolate layer III pyramidal neurons from postmortem human prefrontal cortex Brodmann area 9 (BA9) tissue. Single population RNA-sequencing was conducted utilizing tissue from subjects across the AD spectrum, including individuals with no cognitive impairment (NCI), mild cognitive impairment (MCI), and AD. Differentially expressed genes (DEGs) were compared and contrasted across groups. The number of DEGs increased from Prodromal (MCI versus NCI; 1,306 DEGs) to Progression (AD versus MCI; 2,505 DEGs) to Frank AD (AD versus NCI; 3,259 DEGs). Bioinformatic inquiry revealed alterations in key pathways during disease progression including oxidative phosphorylation, mitochondrial dysfunction, and immune responses suggesting dysfunctional bioenergetics in vulnerable corticocortical projection neurons. The majority of DEGs and pathways shared between Prodromal and Progression exhibited a change in the direction of dysregulation, termed ‘directionally divergent’. In contrast, the majority of common DEGs and pathways between the later stage Progression and Frank AD remained in the same direction, termed ‘directionally convergent’. Candidate genes and pathways were identified that demarcate early-stage AD onset (Prodromal) differentially from AD progression (Progression and Frank AD) providing a roadmap to study cortical cellular vulnerability and key targets for intervention at early stages of AD.
This dataset
Open GSE285831 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 GSE285831_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 PRJNA1206164 and SRA study SRP555161. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
20 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 20 sample titles: 20 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

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.