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Pervasive Enhanced Transcription in Inflammatory Breast Cancer Tumors and PBMCs Impacts RNA Splicing and Intronic RNAs in Plasma

GSE325047 Homo sapiens (human) RNA-seq (gene expression) 80 samples Submitted 2026/05/01 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 80 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
80 samples: 10 conditions, mostly with about 10 replicates eachGroups 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
Pervasive enhanced transcription in inflammatory breast cancer tumors and PBMCs impacts RNA splicing and intronic RNAs in plasmaScience advances · 2026
Summary (written by the submitters)
Inflammatory breast cancer (IBC), the most aggressive and lethal breast cancer subtype, lacks unequivocal genomic differences or robust biomarkers that differentiate it from non-IBC. Here, Thermostable Group II Intron Reverse Transcriptase sequencing of RNA samples revealed myriad differences in tumors, PBMCs, and plasma that distinguished IBC from non-IBC patients and healthy donors across all tested non-IBC subtypes.
Read the full summary ↓
By mapping reads to genome and transcriptome reference sequences and quantitating intron-to-exon read depth ratios, we developed methods for parallel analysis of transcriptional and post-transcriptional gene regulation. This analysis identified numerous protein-coding genes in IBC patient tumors and PBMCs with high intron-to-exon read depths, suggesting rate-limiting RNA splicing that negatively impacts mRNA production. Mirroring gene expression differences in tumors and PBMCs, over-represented protein-coding gene RNAs in IBC patient plasma were largely intron RNA fragments, while those in non-IBC patient and healthy donor plasma were largely mRNA fragments. Our findings provide new insights into IBC and should enable monitoring disease progression by liquid biopsy.
Published in
Pervasive enhanced transcription in inflammatory breast cancer tumors and PBMCs impacts RNA splicing and intronic RNAs in plasma
Wylie D, Wang X, Yao J et al. · Science advances 2026 · PMID 42066072 · doi:10.1126/sciadv.adu0031
This dataset
Open GSE325047 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 GSE325047_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 PRJNA954747 and SRA study SRP432168. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42066072) ↗
Study design
10 conditions, mostly with about 10 replicates each
Healthy PBMC, dono ×13 Healthy Plasma, dono ×13 Breast tissue FFPE, IBC patient ×10 PBMC, IBC patient ×10 Plasma, IBC patient ×10 PBMC, breast cancer patient ×6 Plasma, breast cancer patient ×6 Frozen breast tissue, matched healthy tissue,… ×4 +2 more

Supports a case/control comparison: 50 samples read as cases, 26 as controls.

How we read this: 10 replicated groups read from 80 sample titles; they account for 80 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

+ 40 more — browse all 80 samples with per-sample file links →

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.