Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages (in vivo ATAC-Seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 15 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)
- Samples
- 15 samples: 5 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
- Functional Genetic Screens Reveal Key Pathways Instructing the Molecular Phenotypes of Tumor-Associated MacrophagesCancer immunology research · 2025
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 GSE269029_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 PRJNA1119984 and SRA study SRP511632. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8305309 4T1-Mono, Replicate1 4T1-Mono,
- GSM8305310 4T1-Mono, Replicate2 4T1-Mono,
- GSM8305311 4T1-Mono, Replicate3 4T1-Mono,
- GSM8305312 4T1-Angio, Replicate1 4T1-Angio,
- GSM8305313 4T1-Angio, Replicate2 4T1-Angio,
- GSM8305314 4T1-Angio, Replicate3 4T1-Angio,
- GSM8305315 4T1-MHC-II, Replicate1 4T1-MHC-II,
- GSM8305316 4T1-MHC-II, Replicate2 4T1-MHC-II,
- GSM8305317 4T1-MHC-II, Replicate3 4T1-MHC-II,
- GSM8368212 MC38-Angio, Replicate1 MC38-Angio,
- GSM8368213 MC38-Angio, Replicate2 MC38-Angio,
- GSM8368214 MC38-Angio, Replicate3 MC38-Angio,
- GSM8368215 MC38-MHC-II, Replicate1 MC38-MHC-II,
- GSM8368216 MC38-MHC-II, Replicate2 MC38-MHC-II,
- GSM8368217 MC38-MHC-II, Replicate3 MC38-MHC-II,
- GSE237783 Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [RNA-Seq] 28 samples shares tumor-associated, tumor-derived, interaction, macrophages, phenotypes, instructs, specific
- GSE306916 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages [ATAC-seq] 12 samples shares tumor-associated, macrophages, atac-seq
- GSE281498 The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+ T cells through the direct interaction with IRF4 (ATAC-seq) 20 samples shares interaction, atac-seq
- GSE252269 Targeting the FOXP3–T-bet interaction to restore Treg stability in IFN-γ–driven autoimmunity [CUT&Tag/ATAC-seq] 18 samples shares interaction, atac-seq
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares tumor-associated, macrophages
- GSE290434 A stress response axis in tumor-associated macrophages dictates phenotype heterogeneity and immunotherapy evasion 21 samples shares tumor-associated, macrophages
- GSE324935 IFN-γ and TLR9 signaling reprogram tumor-associated macrophages to promote antitumor immunity in melanoma 20 samples shares tumor-associated, macrophages
- GSE302734 Single-Cell RNA Sequencing Unravels Interactions between Macrophages and Fibroadipogenic Progenitors during Ectopic Bone Formation in FOP Mice 12 samples shares interaction, macrophages
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.