Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 92 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
- Homo sapiens (human)
- Samples
- 92 samples: 24 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
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 GSE269031_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 PRJNA1119981 and SRA study SRP511627. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 6 as controls.
How we read this: 24 replicated groups read from 92 sample titles; they account for 90 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.
- GSM8305253 LGP,CROP-seq
- GSM8305254 LGP-sgRNA,CROP-seq
- GSM8305255 ctrl, Replicate1 ctrl,
- GSM8305256 ctrl, Replicate2 ctrl,
- GSM8305257 ctrl, Replicate3 ctrl,
- GSM8305258 L, Replicate1 L,
- GSM8305259 L, Replicate2 L,
- GSM8305260 L, Replicate3 L,
- GSM8305261 P, Replicate1 P,
- GSM8305262 P, Replicate2 P,
- GSM8305263 P, Replicate3 P,
- GSM8305264 G, Replicate1 G,
- GSM8305265 G, Replicate2 G,
- GSM8305266 G, Replicate3 G,
- GSM8305267 LP, Replicate1 LP,
- GSM8305268 LP, Replicate2 LP,
- GSM8305269 LP, Replicate3 LP,
- GSM8305270 LG, Replicate1 LG,
- GSM8305271 LG, Replicate2 LG,
- GSM8305272 LG, Replicate3 LG,
- GSM8305273 GP, Replicate1 GP,
- GSM8305274 GP, Replicate2 GP,
- GSM8305275 GP, Replicate3 GP,
- GSM8305276 LGP, Replicate1 LGP,
- GSM8305277 LGP, Replicate2 LGP,
- GSM8305278 LGP, Replicate3 LGP,
- GSM8305279 4T1 tumor conditioned medium, Replicate1 4T1 tumor conditioned m…
- GSM8305280 4T1 tumor conditioned medium, Replicate2 4T1 tumor conditioned m…
- GSM8305281 4T1 tumor conditioned medium, Replicate3 4T1 tumor conditioned m…
- GSM8305282 sgNC1, Replicate1 sgNC1,
- GSM8305283 sgNC1, Replicate2 sgNC1,
- GSM8305284 sgNC1, Replicate3 sgNC1,
- GSM8305285 1-sgNC1, Replicate1 1-sgNC1,
- GSM8305286 1-sgNC1, Replicate2 1-sgNC1,
- GSM8305287 1-sgNC1, Replicate3 1-sgNC1,
- GSM8305288 sgLamtor1, Replicate1 sgLamtor1,
- GSM8305289 sgLamtor1, Replicate2 sgLamtor1,
- GSM8305290 sgLamtor1, Replicate3 sgLamtor1,
- GSM8305291 2-sgNC1, Replicate1 2-sgNC1,
- GSM8305292 2-sgNC1, Replicate2 2-sgNC1,
+ 52 more — browse all 92 samples with per-sample file links →
- GSE217847 IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer 136 samples shares tumor-associated, macrophages
- GSE307006 Interferon-γ mediated species-specific immune responses in macrophages to Mycobacterium tuberculosis 37 samples shares macrophages, specific
- GSE242839 PD-1 is induced on tumor-associated macrophages in obesity to directly restrain anti-tumor immunity 29 samples shares tumor-associated, macrophages
- GSE338103 Linker histone H1.0 and JUNB Interaction Maintains Lineage-Specific and Age-Dependent Chromatin Architecture to Safeguard Cell Identity [ATAC-seq] 14 samples shares interaction, specific
- GSE296242 Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions 81 samples shares interaction
- GSE307351 Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions 890 samples shares interaction
- GSE243750 SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE 288 samples shares interaction
- GSE262989 Psychedelic control of neuroimmune interactions governing fear 108 samples shares interaction
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.