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The Notch ligand Jagged1 regulates extracellular matrix production and organization in triple-negative breast cancer

GSE296927 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/02/09 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)
Topic
Breast cancerThis series is part of our curated briefing on it.
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.
Paper
Jagged1 regulates extracellular matrix deposition and remodeling in triple-negative breast cancerScience advances · 2026
Summary (written by the submitters)
The extracellular matrix (ECM) in the tumor microenvironment plays an essential role in the progression of cancer. Here, we show that expression of the Notch ligand Jagged1 correlates with poor patient survival in aggressive breast cancer and that Jagged1 promotes in vivo tumor growth and invasion of triple-negative breast cancer cells.
Read the full summary ↓
Using transcriptomics, proteomics, and imaging approaches of cancer cell/fibroblast co-cultures, both in vitro and in vivo, we demonstrate that Jagged1 drives fibroblast activation, increased collagen deposition, and aligned organization of ECM fibers. Jagged1 increases transforming growth factor beta (TGFβ) related signaling in fibroblast co-cultures and the Jagged1-induced ECM alignment can be prevented by a TGFβ inhibitor. Thus, Jagged1 regulates ECM remodeling upstream of TGFβ. With the emergence of safe therapeutics targeting specific Notch ligands and receptors, Jagged1 modulation may offer a path to therapeutically target invasive breast cancer.
Published in
Jagged1 regulates extracellular matrix deposition and remodeling in triple-negative breast cancer
Parikainen M, Suwal U, Rappu P et al. · Science advances 2026 · PMID 41849611 · doi:10.1126/sciadv.aea9562
This dataset
Open GSE296927 in finder → Find more human RNA-seq datasets → Breast cancer 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 GSE296927_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 PRJNA1261943 and SRA study SRP584708. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41849611) ↗
Study design
6 conditions, mostly in triplicate
MDA-MB-231 Jag1KO cells, 3D Matrigel culture,… ×3 MDA-MB-231 Jag1KO+rescue cells, 3D Matrigel c… ×3 MDA-MB-231 Jag1KO+ctrl cells, 3D Matrigel cul… ×3 MDA-MB-231 siCtrl cells, 3D Matrigel culture,… ×3 MDA-MB-231 siJag1 cells, 3D Matrigel culture,… ×3 MDA-MB-231 WT cells, 3D Matrigel culture, biol ×2 MDA-MB-231 WT cells, 3D Matrigel culture, bi… ×1

Supports a between-group comparison across 17 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 17 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 Breast cancer datasets

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