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Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer’s disease neuropathology [RNA-seq]

GSE287651 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/01/22 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 4 × NeuN+/RBFOX1+ Entorhinal CERAD_B Braak_II vs 4 × NeuN+/RBFOX1- Entorhinal CERAD_0 Braak_0 vs 4 × NeuN+/RBFOX1- Entorhinal CERAD_B Braak_II vs 3 × NeuN+/RBFOX1+ Entorhinal CERAD_0 Braak_0Groups 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)
Neurons located in the layer II of the entorhinal cortex (ECII) are the primary site of pathological tau accumulation and neurodegeneration at preclinical stages of Alzheimer's disease (AD). Exploring the alterations that underlie the early degeneration of these cells is essential to develop therapies that delay disease onset. Here we performed cell–type specific profiling of the EC at the onset of human AD neuropathology.
Read the full summary ↓
We identify an early response to amyloid pathology by microglia and oligodendrocytes. More importantly, we find that the Reelin signaling pathway is already impaired at this early disease stage, particularly in ECII neurons. This indicates that dysregulation of this pathway, with emerging genetic association with AD, plays a pivotal role in the selective vulnerability of the EC and in the onset of AD neuropathology.
This dataset
Open GSE287651 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 GSE287651_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 PRJNA1214194 and SRA study SRP559003. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × NeuN+/RBFOX1+ Entorhinal CERAD_B Braak_II vs 4 × NeuN+/RBFOX1- Entorhinal CERAD_0 Braak_0 vs 4 × NeuN+/RBFOX1- Entorhinal CERAD_B Braak_II vs 3 × NeuN+/RBFOX1+ Entorhinal CERAD_0 Braak_0

Supports a between-group comparison across 15 samples.

How we read this: 4 replicated groups read from 15 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.