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Tumor Cell JAGGED-1 Promotes Lymph Node Metastasis and Predicts Recurrence in Lymph Node Positive Breast Cancer Patients

GSE253036 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2026/07/23 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 8 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
Tumor cell Jagged-1 promotes regional lymphatic metastasis and predicts recurrence in node-positive breast cancerBreast cancer research : BCR · 2026
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Tumor cell Jagged-1 promotes regional lymphatic metastasis and predicts recurrence in node-positive breast cancer
Gordon B, Swaminathan B, Youn SW et al. · Breast cancer research : BCR 2026 · PMID 42321861 · doi:10.1186/s13058-026-02331-7
This dataset
Open GSE253036 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 GSE253036_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 PRJNA1063681 and SRA study SRP482957. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42321861) ↗
Study design
8 conditions, mostly in triplicate
MDA-MB-231-D3H2LN cells expressing JAG1 ×3 MDA-MB-231-D3H2LN with JAG1 KO ×3 MDA-MB-231-D3H2LN with JAG1 KO + JAG1 OE (res… ×3 HdLEC Control ×3 HdLEC JAG1 stimulated ×3 MDA-MB-231 cells ×3 MDA-MB-231-D3H2LN (MDA231LN) ×3 MDA-MB-231-D3H2LN cells with CRISPR/Cas9 JAG1… ×2 +4 more

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

How we read this: 8 replicated groups read from 27 sample titles; they account for 23 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

Search all human RNA-seq datasets in GEO →

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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.