GEO series

Identifying THAP1 target genes in HEK-293T cells

GSE264536 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/01/18 Platform GPL20301

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
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: Loss-of-function mutations in the dystonia gene THAP1 impair proteasome function by inhibiting PSMB5 expressionNature communications · 2025

Summary (written by the submitters)

The 26S proteasome is a multi-catalytic protease that serves as the endpoint for protein degradation via the ubiquitin-proteasome system. Proteasome function requires the concerted activity of 33 distinct gene products, but how the expression of proteasome subunits is regulated in mammalian cells remains poorly understood. Leveraging coessentiality data from the DepMap project, here we characterize an essential role for the Dystonia gene THAP1 in maintaining the basal expression of PSMB5.

Read the full summary ↓

PSMB5 insufficiency resulting from loss of THAP1 leads to defects in proteasome assembly, impaired proteostasis and cell death. The toxicity associated with loss of THAP1 can be rescued upon exogenous expression of PSMB5, explaining the molecular basis for their coessentiality. Leveraging a fluorescent reporter knocked-in to the endogenous PSMB5 locus, we define the transcriptional targets of THAP1 through RNA-seq analysis and perform a deep mutational scan to systematically assess the function of thousands of single amino acid THAP1 variants. Altogether, these data identify THAP1 as a new regulator of proteasome function and suggest that aberrant proteostasis may contribute to the pathogenesis of THAP1 Dystonias.

Published in

Loss-of-function mutations in the dystonia gene THAP1 impair proteasome function by inhibiting PSMB5 expression

Ramage DE, Grant DW, Timms RT · Nature communications 2025 · PMID 39929834 · doi:10.1038/s41467-025-56782-1

This dataset

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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 GSE264536_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 PRJNA1103109 and SRA study SRP503269. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39929834) ↗

Samples in this study

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+ 15 more — browse all 15 samples with per-sample file links →

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