← BioTransfer GEO Dataset Finder
GEO series

TDP-43 nuclear loss in FTD-ALS causes widespread alternative polyadenylation

GSE252892 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/11/20 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × iNeuron, shControl, day 7, RNA-seq, vs 3 × iNeuron, shTDP-43, day 7, RNA-seq, vs 3 × iNeuron, shControl, day 7, 3'end-seq, vs 3 × iNeuron, shTDP-43, day 7, 3'end-seq,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.
Paper
TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changesNature neuroscience · 2025
Summary (written by the submitters)
In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is depleted from the nucleus. TDP-43 loss leads to cryptic exon inclusion but a role in other RNA processing events remains unresolved. Here, we show that loss of TDP-43 causes widespread changes in alternative polyadenylation, impacting expression of disease-relevant genes (e.g., ELP1, NEFL, and TMEM106B), providing evidence that alternative polyadenylation is a new facet to TDP-43 pathology.
Published in
TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes
Zeng Y, Lovchykova A, Akiyama T et al. · Nature neuroscience 2025 · PMID 41120750 · doi:10.1038/s41593-025-02049-3
This dataset
Open GSE252892 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 GSE252892_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 PRJNA1063175 and SRA study SRP482832. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41120750) ↗
Study design
3 × iNeuron, shControl, day 7, RNA-seq, vs 3 × iNeuron, shTDP-43, day 7, RNA-seq, vs 3 × iNeuron, shControl, day 7, 3'end-seq, vs 3 × iNeuron, shTDP-43, day 7, 3'end-seq,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

Search all human RNA-seq datasets in GEO →

Share this dataset

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.