GEO series

IGF2BP3 regulates RNA metabolism during unfolded protein response [RNA-Seq]

GSE289424 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/07/23 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 6 conditions, mostly in triplicateGroups 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)

Accumulation of misfolded proteins in the endoplasmic reticulum (ER) perturbs cellular homeostasis and leads to pathological conditions termed ER stress. The Unfolded Protein Response (UPR) is a highly conserved signaling cascade that maintains ER homeostasis. While the transcriptional response is paramount for UPR signaling, several mRNAs are regulated at the posttranscriptional level, yet how this is achieved remains poorly understood.

Read the full summary ↓

Here, we show that a highly conserved RNA-binding protein, IGF2BP3, interacts with transcripts encoding for the UPR target genes and regulates the UPR signaling. During ER stress, IGF2BP3 destabilized most of its targets, including the UPR target RNAs. On the other hand, IGF2BP3 stabilized a subset of mRNAs encoding for transcription regulators through this indirectly regulated transcription of the UPR target genes. This feedback loop allows IGF2BP3 to elevate the levels of stress response genes while leading to the degradation of other transcripts during ER stress. Our results reveal a novel IGF2BP3-driven gene regulatory network contributing to cellular adaptation to ER stress.

This dataset

Open GSE289424 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 GSE289424_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 PRJNA1222889 and SRA study SRP563568. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

siControl, DMSO control, ×3 siControl, ER stress, ×3 siIGF2BP2, DMSO control, ×3 siIGF2BP2, ER stress, ×3 siIGF2BP3, DMSO control, ×3 siIGF2BP3, ER stress, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM8791291 siControl, DMSO control, 1 siControl, DMSO control,
GSM8791292 siControl, DMSO control, 2 siControl, DMSO control,
GSM8791293 siControl, DMSO control, 3 siControl, DMSO control,
GSM8791294 siControl, ER stress, 1 siControl, ER stress,
GSM8791295 siControl, ER stress, 2 siControl, ER stress,
GSM8791296 siControl, ER stress, 3 siControl, ER stress,
GSM8791297 siIGF2BP2, DMSO control, 1 siIGF2BP2, DMSO control,
GSM8791298 siIGF2BP2, DMSO control, 2 siIGF2BP2, DMSO control,
GSM8791299 siIGF2BP2, DMSO control, 3 siIGF2BP2, DMSO control,
GSM8791300 siIGF2BP2, ER stress, 1 siIGF2BP2, ER stress,
GSM8791301 siIGF2BP2, ER stress, 2 siIGF2BP2, ER stress,
GSM8791302 siIGF2BP2, ER stress, 3 siIGF2BP2, ER stress,
GSM8791303 siIGF2BP3, DMSO control, 1 siIGF2BP3, DMSO control,
GSM8791304 siIGF2BP3, DMSO control, 2 siIGF2BP3, DMSO control,
GSM8791305 siIGF2BP3, DMSO control, 3 siIGF2BP3, DMSO control,
GSM8791306 siIGF2BP3, ER stress, 1 siIGF2BP3, ER stress,
GSM8791307 siIGF2BP3, ER stress, 2 siIGF2BP3, ER stress,
GSM8791308 siIGF2BP3, ER stress, 3 siIGF2BP3, ER stress,

Datasets on a similar topic

GSE274188 RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages [RNA-Seq and Ribo-Seq] 12 samples shares protein, rna-seq
GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares rna-seq
GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares rna-seq
GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares rna-seq
GSE297742 Bulk RNA-seq of primary tumor biopsy samples from prostate adenocarcinoma patients 234 samples shares rna-seq
GSE295173 Multi-modal single-cell sequencing reveals network transition in circulating monocytes that aligns with faster recovery in trauma patients and favors a response to M-CSF [scRNA-Seq] 30 samples shares rna-seq
GSE294272 Tumor-resident T cells and dendritic cells form an in situ archetype for immunotherapy response in melanoma [bulk RNA-seq] 29 samples shares rna-seq
GSE293805 Single nucleus RNA-sequencing atlas of pediatric solid tumors 182 samples shares rna-seq

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.