TREM2+ Macrophage Infiltration Underlies Breast Cancer Lung Metastasis due to Paclitaxel Treatment [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 8 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 8 samples: 8 samples, each with a distinct title — no replicated groupsGroups 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
- Paclitaxel drives TREM2(+) macrophage expansion underlying its inferior therapeutic efficacy compared to Nab-paclitaxelNature communications · 2026
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE295918_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1256778 and SRA study SRP582111. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 8 sample titles: 8 distinct titles with little repetition. 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.
- GSM8960870 BT549 cell, DMSO
- GSM8960871 BT549 cell, Paclitaxe
- GSM8960872 BT549 cell, PBS
- GSM8960873 BT549 cell, Nab-Paclitaxe
- GSM8960874 BMDM, DMSO
- GSM8960875 BMDM, Paclitaxe
- GSM8960876 BMDM, PBS
- GSM8960877 BMDM, Nab-Paclitaxe
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing
- GSE300053 Phase separation of endothelial PML drives inflammatory macrophage infiltration during liver fibrosis 69 samples shares infiltration, macrophage
- GSE293117 GPR34 loss-of-function rescues TREM2 metabolic dysfunction and promotes responsive microglial states 56 samples shares trem2
- GSE287346 MafB is a conserved transcriptional regulator of macrophage development and identity across tissues and species [CUT&Run] 33 samples shares macrophage
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.