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Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells

GSE282654 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2025/04/07 Platform GPL16791
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)
Samples
27 samples: 9 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
Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cellsiScience · 2025
Summary (written by the submitters)
Cellular phenotypes are dictated not by single signals but by the integration of multiple extracellular cues, a process that remains poorly understood. Here, we systematically dissect how combinations of Oncostatin M, Transforming Growth Factor β1, and Epidermal Growth Factor shape the behavior of MCF10A mammary epithelial cells. Live-cell imaging revealed that ligand combinations drive emergent phenotypes absent in single-ligand contexts, pointing to the induction of novel molecular programs.
Read the full summary ↓
Transcriptomic profiling uncovered synergistically regulated genes, while partial least-squares regression linked these transcriptional signatures to quantitative imaging-derived phenotypes and validated them across independent datasets. Functional analysis revealed CXCR2 signaling, upregulated through CREB activation, as a key driver of enhanced cell motility under combinatorial ligand treatment. Together, these findings establish a framework for uncovering how extracellular signals converge to modulate gene expression and phenotype, providing new insight into the principles governing complex epithelial cell behaviors.
Published in
Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells
McLean IC, Gross SM, Copperman J et al. · iScience 2025 · PMID 41054517 · doi:10.1016/j.isci.2025.113407
This dataset
Open GSE282654 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 GSE282654_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 PRJNA1189550 and SRA study SRP547047. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41054517) ↗
Study design
9 conditions, mostly in triplicate
MCF10A_T0Ctrl ×3 MCF10A_PBS ×3 MCF10A_EGF ×3 MCF10A_EGFTGFB ×3 MCF10A_OSM ×3 MCF10A_TGFB ×3 MCF10A_OSMTGFB ×3 MCF10A_EGFOSM ×3 +1 more

Supports a between-group comparison across 27 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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
Datasets on a similar topic

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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.