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Global identification of ER stress-regulated RNA binding Proteins in clonal pancreatic beta-cells, reveals an important role for DEAD-box helicase 3 X-linked (DDX3X) in the execution of the Unfolded Protein Response and the determination of cell fate.

GSE304391 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/08/07 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 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
Mus musculus (mouse)
Samples
12 samples: 3 × MIN6 cells shCONTROL (PLKO1), 24h CPA treated n= vs 3 × MIN6 cells shDDX3X (DDX3X1), 24h DMSO Vehicle control n= vs 3 × MIN6 cells shDDX3X (DDX3X), 24h CPA treated n=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.
Summary (written by the submitters)
Endoplasmic reticulum (ER) stress plays an important role in pancreatic β-cell dysfunction and death, contributing to both type 1 and type 2 diabetes. The Unfolded Protein Response (UPR) is a key adaptive mechanism that helps cells cope with ER stress by altering gene expression. RNA-binding proteins (RBPs), which regulate gene expression at multiple levels, are likely to influence the UPR, yet their role in the UPR remain largely unexplored.
Read the full summary ↓
To investigate this, we examined global changes in RBP-RNA interactions in the mouse β-cell line MIN6 under ER stress. This analysis identified 339 RBPs, with 13 showing significant changes in RNA binding. Among these, DEAD-box helicase 3 X-linked (DDX3X) emerged as a candidate for further study. Functional experiments revealed that inhibiting or knocking down DDX3X in MIN6 cells suppressed the ER stress-induced expression of the pro-apoptotic protein CHOP and its upstream regulator ATF4. Transcriptomic profiling of DDX3X-deficient MIN6 cells showed that DDX3X is essential not only for the upregulation of CHOP but also 24 other ER stress-responsive genes, including apoptosis-related genes such as Bcl2 and Bid. Notably, DDX3X knockdown conferred partial protection against ER stress-induced cytotoxicity and improved cell viability. In summary, these findings reveal widespread changes in the RBP landscape during ER stress in β-cells and highlight DDX3X as a key regulator of the UPR. DDX3X promotes the expression of stress-responsive genes and contributes to β-cell death under chronic ER stress, suggesting it may be a potential therapeutic target in diabetes.
This dataset
Open GSE304391 in finder → Find more mouse 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 GSE304391_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 PRJNA1301241 and SRA study SRP606402. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × MIN6 cells shCONTROL (PLKO1), 24h CPA treated n= vs 3 × MIN6 cells shDDX3X (DDX3X1), 24h DMSO Vehicle control n= vs 3 × MIN6 cells shDDX3X (DDX3X), 24h CPA treated n=

Supports a case/control comparison: 3 samples read as cases, 6 as controls.

How we read this: 3 replicated groups read from 12 sample titles; they account for 9 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
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