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Unbiased niche labeling maps immune-excluded niche in bone metastasis

GSE296725 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/04/28 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 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
Mus musculus (mouse)
Samples
24 samples: 12 conditions, mostly in duplicateGroups 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
Unbiased niche labeling maps immune-excluded niche in bone metastasisCell · 2026
Summary (written by the submitters)
Microenvironment niches determine cellular fates of metastatic cancer cells. However, robust and unbiased approaches to identify niche components and their molecular profiles are lacking. We established Sortase A-Based Microenvironment Niche Tagging (SAMENT), which selectively labels cells encountered by cancer cells during metastatic colonization.
Read the full summary ↓
SAMENT was applied to multiple cancer models colonizing the same organ and the same cancer to different organs. Common niche features include macrophage enrichment and T cell depletion. Macrophage niches are phenotypically diverse in different organs. In bone, niche macrophages express estrogen receptor (ER) and exhibit active ER signaling in male and female hosts. Conditional knockout of ER in macrophages significantly retarded bone colonization by allowing T cell infiltration. ER expression was also discovered in human bone metastases of both genders. Collectively, we identified a unique population of ER+ macrophages in metastatic niche and functionally tie ER signaling in macrophages to T cell exclusion during metastatic colonization.
Published in
Unbiased niche labeling maps immune-excluded niche in bone metastasis
Xu Z, Liu F, Ding Y et al. · Cell 2026 · PMID 42054994 · doi:10.1016/j.cell.2026.04.009
This dataset
Open GSE296725 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 GSE296725_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 PRJNA1096642 and SRA study SRP499917. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42054994) ↗
Study design
12 conditions, mostly in duplicate
CKDL240027296_CKDL240027298_m306_LysM_ctrl_Fe… ×2 CKDL240027296_CKDL240027298_m307_LysM_ctrl_Fe… ×2 CKDL240027296_CKDL240027298_m309_LysM_ctrl_Fe… ×2 CKDL240027296_CKDL240027298_m319_LysM_ctrl_Ma… ×2 CKDL240027296_CKDL240027298_m320_LysM_ctrl_Ma… ×2 CKDL240027296_CKDL240027298_m324_LysM_ctrl_Ma… ×2 CKDL240027297_CKDL240027299_m311_LysM_cre_Male ×2 CKDL240027297_CKDL240027299_m313_LysM_cre_Male ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 12 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
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