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Proteasome activity maintains cell type-specific gene expression

GSE309969 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2026/01/09 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 4 × HCT116 WTscramble vs 4 × HCT116 WTsiOTUD5 vs 4 × HCT116 ΔUIMscramble vs 4 × HCT116 ΔUIM scrambleGroups 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)
Regulated proteolysis in eukaryotes relies on the ubiquitin-proteasome system, which is critical to myriad cellular functions, including protein quality control, cell cycle regulation, and DNA repair. Here, we provide evidence that proteasome activity is also essential for maintaining cell identity. This discovery was made by evaluating the impact of losing the ubiquitin-binding activity of proteasome substrate receptor hRpn10/PSMD4.
Read the full summary ↓
The most dysregulated proteins in cells that express hRpn10 truncated before its ubiquitin interaction motifs (ΔUIM) are transcriptionally altered, with striking overrepresentation of proteins canonically restricted in expression to specific tissues. This dysregulation is partly driven by accumulation of the proteasome substrate anddeubiquitinase OTUD5, a known chromatin and transcriptional regulator. Our results thus identify previously unrecognized proteasome-dependent mechanisms to safeguard cell-type specific gene expression programs and expand proteasome biology to include governance of cell identity.
This dataset
Open GSE309969 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 GSE309969_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 PRJNA1364067 and SRA study SRP645404. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × HCT116 WTscramble vs 4 × HCT116 WTsiOTUD5 vs 4 × HCT116 ΔUIMscramble vs 4 × HCT116 ΔUIM scramble

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
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.