← BioTransfer GEO Dataset Finder
GEO series

Bulk RNA-sequencing after estrogen-related receptorr knockdown (ESRRA) knockdown in human GIST-T1 cell line

GSE330412 Homo sapiens (human) RNA-seq (gene expression) 9 samples Submitted 2026/07/17 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 9 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)
Topic
Gastrointestinal stromal tumourThis series is part of our curated briefing on it.
Samples
9 samples: 3 × T1-NONTARGET1_S vs 3 × T1-ESRRA-KD1_S vs 3 × T1-NONTARGETplusIMA1-48H_SGroups 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
Estrogen-related receptor alpha (ERRα) promotes gastrointestinal stromal tumor progression and epithelial-mesenchymal transition through Wnt/β-cateninResearch square · 2026
Summary (written by the submitters)
Gastrointestinal stromal tumor (GIST) is the most common sarcoma and primarily driven by a gain-of-function mutation in either the KIT or PDGFRA receptor tyrosine kinase. Estrogen-related receptor alpha (ERRα, encoded by ESRRA) is an orphan nuclear receptor whose role in GIST is unknown. We found that ERRα was highly expressed in human GIST cell lines and human GIST surgical specimens.
Read the full summary ↓
Pharmacologic inhibition of ERRα using XCT90 or siRNA-mediated knockdown reduced viability, colony formation, and migration of human GIST cell lines.To further examine ERRα's role in regulating gene transcription in human GIST, we performed RNA-sequencing after siRNA-mediated knockdown of ERRα to identify changes in mRNA expression. We also sequenced T1 cells after imatinib treatment to compare the two treatments with each other in addition to the non-target controls.
Published in
Estrogen-related receptor alpha (ERRα) promotes gastrointestinal stromal tumor progression and epithelial-mesenchymal transition through Wnt/β-catenin
DeMatteo R, Hartlein T, Zeng S et al. · Research square 2026 · PMID 42396531 · doi:10.21203/rs.3.rs-9930164/v1
This dataset
Open GSE330412 in finder → Find more human RNA-seq datasets → Gastrointestinal stromal tumour landscape →
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 GSE330412_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 PRJNA1463807 and SRA study SRP698743. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42396531) ↗
Study design
3 × T1-NONTARGET1_S vs 3 × T1-ESRRA-KD1_S vs 3 × T1-NONTARGETplusIMA1-48H_S

Supports a between-group comparison across 9 samples.

How we read this: 3 replicated groups read from 9 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
More Gastrointestinal stromal tumour datasets

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.