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The effect of co-culture on MMTV-HER2 early lesion or primary tumor cell and alveolar macrophages [bulk RNA-seq]

GSE278443 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2024/09/30 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 22 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
Mus musculus (mouse)
Samples
22 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
Lung-resident alveolar macrophages regulate the timing of breast cancer metastasisCell · 2024
Summary (written by the submitters)
Disseminated cancer cells reside in the lung alveolar niche where they are exposed to interactions with alveolar macrophages. Here we report bulk RNA-sequencing data from co-cultured MMTV-HER2 mammary early lesion cells or mammary primary tumor cells cultured with lung alveolar macrophages. We discovered reciprocal regulation between mammary cells and alveolar macrophages, where early lesion cells instruct alveolar macrophages to maintain an anti-tumor phenotype and alveolar macrophages activate an epithelial to mesenchymal program in early lesion cells.
Read the full summary ↓
Coveresely, primary tumor cells activate inflammatory prorgams in alveolar macrophages, while alveolar macrophages are not able to activate growth restriction programs in primary tumor cells. Receptor-ligand analysis highlighted two known pathways invovled in quiencesce, namely the TGF-beta pathway and the OSM pathway.
Published in
Lung-resident alveolar macrophages regulate the timing of breast cancer metastasis
Dalla E, Papanicolaou M, Park MD et al. · Cell 2024 · PMID 39378878 · doi:10.1016/j.cell.2024.09.016
This dataset
Open GSE278443 in finder → Find more mouse 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 GSE278443_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 PRJNA1167276. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39378878) ↗
Study design
8 conditions, mostly in triplicate
Early lesion cells from mono-culture, ×3 Early lesion cells from co-culture with alveo… ×3 Alveolar macrophage from mono-culture control… ×3 Alveolar macrophage from co-culture with epri… ×3 Primary tumor cells from mono-culture, ×3 Primary tumor cells from co-culture with alve… ×3 Alveolar macrophage from mono-culture from ea… ×2 Alveolar macrophage from co-culture with earl… ×2

Supports a between-group comparison across 22 samples.

How we read this: 8 replicated groups read from 22 sample titles; they account for 22 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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