GEO series

Macrophage and Triple-Negative Breast Cancer Cell Phenotype Changes in a 3D Co-Culture Model

GSE304137 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2026/08/03 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 6 conditions, mostly with about 4 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.

Summary (written by the submitters)

Tumor-associated macrophage (TAM) infiltration is a characteristic of triple-negative breast cancer (TNBC) related to drug resistance and poor prognosis. Unraveling intricate cell-cell interactions in the tumor microenvironment (TME) remains challenging, especially when using a standardized 3D culture system. This study used the TNBC cell line, MDA-MB-231, and polarized M1-like or M2-like macrophages derived from THP-1 monocytes to establish 3D co-culture spheroids for mimicking the TME environment.

Read the full summary ↓

Drug efficacy, epithelial-mesenchymal transition (EMT) in cancer cells, macrophage phenotypes, and RNA sequencing of spheroids were performed. We observed that M2 macrophages increased the viability and proliferation rate of MDA-MB-231 cells in the 3D spheroids, while both M1 and M2 macrophages increased the chemosensitivity of MDA-MB-231 cells to doxorubicin and paclitaxel. Interestingly, instead of maintaining their phenotypes, M1 and M2 macrophages lost some polarization when 3D co-cultured with MDA-MB-231 cells. Compared with 2D cultures, an expected mesenchymal transition was observed in 3D spheroid MDA-MB-231 cells. However, both M1 and M2 macrophages induced a partial epithelial reversion in co-cultured spheroids. Deconvolution of our bulk RNA sequencing results verified the existence of phenotypic transitions between M1 and M2 macrophages when co-cultured with MDA-MB-231 cells in 3D spheroids. In conclusion, our findings suggest that a 3D co-culture system of polarized macrophages and breast cancer cells can serve as an effective platform for studying the dynamic cellular phenotype changes that occur in a heterogeneous environment contributing to chemoresistance. This 3D co-culture system may provide a valuable tool for drug screening to identify targeted therapies for cancer.

This dataset

Open GSE304137 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 GSE304137_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 PRJNA1299258 and SRA study SRP605679. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 4 replicates each

MDA-MB-231, 2D, sample ×4 MDA-MB-231, 3D, sample ×4 MDA-MB-231 Coculture with M1 Macrophages, sam… ×4 MDA-MB-231 Coculture with M2 Macrophages, sam… ×4 M1 Macrophage, sample ×4 M2 Macrophage, sample ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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

GSM9144234 MDA-MB-231, 2D, sample 1 MDA-MB-231, 2D, sample
GSM9144235 MDA-MB-231, 2D, sample 2 MDA-MB-231, 2D, sample
GSM9144236 MDA-MB-231, 2D, sample 3 MDA-MB-231, 2D, sample
GSM9144237 MDA-MB-231, 2D, sample 4 MDA-MB-231, 2D, sample
GSM9144238 MDA-MB-231, 3D, sample 1 MDA-MB-231, 3D, sample
GSM9144239 MDA-MB-231, 3D, sample 2 MDA-MB-231, 3D, sample
GSM9144240 MDA-MB-231, 3D, sample 3 MDA-MB-231, 3D, sample
GSM9144241 MDA-MB-231, 3D, sample 4 MDA-MB-231, 3D, sample
GSM9144242 MDA-MB-231 Coculture with M1 Macrophages, sample 1 MDA-MB-231 Coculture wi…
GSM9144243 MDA-MB-231 Coculture with M1 Macrophages, sample 2 MDA-MB-231 Coculture wi…
GSM9144244 MDA-MB-231 Coculture with M1 Macrophages, sample 3 MDA-MB-231 Coculture wi…
GSM9144245 MDA-MB-231 Coculture with M1 Macrophages, sample 4 MDA-MB-231 Coculture wi…
GSM9144246 MDA-MB-231 Coculture with M2 Macrophages, sample 1 MDA-MB-231 Coculture wi…
GSM9144247 MDA-MB-231 Coculture with M2 Macrophages, sample 2 MDA-MB-231 Coculture wi…
GSM9144248 MDA-MB-231 Coculture with M2 Macrophages, sample 3 MDA-MB-231 Coculture wi…
GSM9144249 MDA-MB-231 Coculture with M2 Macrophages, sample 4 MDA-MB-231 Coculture wi…
GSM9144250 M1 Macrophage, sample 1 M1 Macrophage, sample
GSM9144251 M1 Macrophage, sample 2 M1 Macrophage, sample
GSM9144252 M1 Macrophage, sample 3 M1 Macrophage, sample
GSM9144253 M1 Macrophage, sample 4 M1 Macrophage, sample
GSM9144254 M2 Macrophage, sample 1 M2 Macrophage, sample
GSM9144255 M2 Macrophage, sample 2 M2 Macrophage, sample
GSM9144256 M2 Macrophage, sample 3 M2 Macrophage, sample
GSM9144257 M2 Macrophage, sample 4 M2 Macrophage, sample

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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.