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Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome

GSE233208 Homo sapiens (human) Spatial transcriptomics 185 samples Submitted 2024/09/12 Platform GPL24676Platform GPL24247
At a glance

Spatial transcriptomics · human · 185 samples

What it is
Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism
Homo sapiens (human)
Samples
185 samples: 148 distinct titles, 29 of them repeatedGroups 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
Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's diseaseNature genetics · 2024
Summary (written by the submitters)
The highly dynamic regulatory networks involved in brain processes can result in specific gene expression patterns across distinct cell types. The single-nucleus and spatial transcriptomics data allow us to better understand these patterns. This study involved the analyses of the brains of mice and humans with Alzheimer’s Disease (AD) and Down Syndrome.
Published in
Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's disease
Miyoshi E, Morabito S, Henningfield CM et al. · Nature genetics 2024 · PMID 39578645 · doi:10.1038/s41588-024-01961-x
This dataset
Open GSE233208 in finder → Find more 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 GSE233208_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA975472 and SRA study SRP439197. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39578645) ↗
Study design
148 distinct titles, 29 of them repeated
Sublibrary_1_S1_L ×3 Sublibrary_2_S2_L ×3 Sublibrary_3_S3_L ×3 Sublibrary_4_S4_L ×3 Sublibrary_5_S5_L ×3 Sublibrary_6_S6_L ×3 Sublibrary_7_S7_L ×3 Sublibrary_8_S8_L ×3 +21 more

How we read this: Read from 185 sample titles: 148 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

+ 145 more — browse all 185 samples with per-sample file links →

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.