GEO series

Alterations in single-cell transcriptomic levels and cellular localisation of hnRNP proteins in Frontotemporal Lobar Degeneration

GSE288106 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2026/03/02 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 16 samples: 5 × CTRL vs 5 × TDPC vs 3 × C9 TDPA vs 3 × TDPAGroups 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: Transcriptomic and pathological analysis of the hnRNP network reveals glial involvement in frontotemporal lobar degeneration pathological subtypesBrain communications · 2026

Summary (written by the submitters)

Frontotemporal dementia (FTD) is a neurodegenerative disorder with a strong heritable component. Frontotemporal lobar degeneration (FTLD) refers to the pathological changes seen in FTD, characterised by atrophy of the frontal and temporal lobes and the presence of abnormal protein inclusions. In the case of FTLD with hyperphosphorylated TDP-43 positive inclusions (FTLD-TDP), five pathological subtypes (A, B, C, D, and E) are observed based on the types and distribution of inclusions found in the brain.

Read the full summary ↓

In all subtypes, there tends to be a large variability in the amount of pathological inclusions observed between cases, with limited correlation to clinical manifestations. TDP-43 is an RNA binding protein belonging to the heterogeneous nuclear ribonucleoprotein (hnRNP) family which along with other hnRNPs modulates multiple aspects of RNA processing. HnRNPs other than TDP-43 have been implicated in several neurological diseases, including ALS, FTLD-TDP, FTLD-FUS and Alzheimer's disease. Multiple hnRNPs have been found in pathological inclusions in specific subtypes of FTLD-TDP, suggesting potential roles in the disease process. The role of the hnRNP network in FTLD disease pathogenesis has not yet been investigated. This study aimed to comprehensively evaluate the presence and expression of hnRNP proteins in two pathological subtypes of sporadic FTLD-TDP (A and C) as well as the genetic form FTLD-TDP A C9orf72 using immunohistochemistry and gene expression analysis by single cell RNA-sequencing. We sought to determine whether hnRNPs exhibited aberrant expression at the protein and transcript level in FTLD cases with TDP-43 pathology.

Published in

Transcriptomic and pathological analysis of the hnRNP network reveals glial involvement in frontotemporal lobar degeneration pathological subtypes

Gatt A, Buhidma Y, Fodder K et al. · Brain communications 2026 · PMID 42327368 · doi:10.1093/braincomms/fcag197

This dataset

Open GSE288106 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 GSE288106_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1216202 and SRA study SRP560950. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42327368) ↗

Study design

5 × CTRL vs 5 × TDPC vs 3 × C9 TDPA vs 3 × TDPA

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

GSM8759021 CTRL1 CTRL
GSM8759022 TDPC1 TDPC
GSM8759023 TDPC2 TDPC
GSM8759024 CTRL2 CTRL
GSM8759025 C9 TDPA1 C9 TDPA
GSM8759026 TDPA1 TDPA
GSM8759027 TDPA2 TDPA
GSM8759028 TDPC3 TDPC
GSM8759029 C9 TDPA2 C9 TDPA
GSM8759030 TDPC4 TDPC
GSM8759031 TDPC5 TDPC
GSM8759032 TDPA3 TDPA
GSM8759033 CTRL3 CTRL
GSM8759034 C9 TDPA3 C9 TDPA
GSM8759035 CTRL4 CTRL
GSM8759036 CTRL5 CTRL

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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.