Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [RNA-Seq]
RNA-seq (gene expression) · mouse · 28 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
- 28 samples: 14 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
- 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 GSE237783_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: 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 PRJNA996603 and SRA study SRP450434. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 2 samples read as cases, 2 as controls.
How we read this: 14 replicated groups read from 28 sample titles; they account for 28 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.
- GSM7653225 M0, Replicate1 M0,
- GSM7653226 M0, Replicate2 M0,
- GSM7653227 4T1, Replicate1 4T1,
- GSM7653228 4T1, Replicate2 4T1,
- GSM7653229 Panc02, Replicate1 Panc02,
- GSM7653230 Panc02, Replicate2 Panc02,
- GSM7653231 Control,Replicate1 Control,
- GSM7653232 Control,Replicate2 Control,
- GSM7653233 LA, Replicate1 LA,
- GSM7653234 LA, Replicate2 LA,
- GSM7653235 GM-CSF, Replicate1 GM-CSF,
- GSM7653236 GM-CSF, Replicate2 GM-CSF,
- GSM7653237 PGE2, Replicate1 PGE2,
- GSM7653238 PGE2, Replicate2 PGE2,
- GSM7653239 LA_PGE2, Replicate1 LA_PGE2,
- GSM7653240 LA_PGE2, Replicate2 LA_PGE2,
- GSM7653241 LA_GM-CSF, Replicate1 LA_GM-CSF,
- GSM7653242 LA_GM-CSF, Replicate2 LA_GM-CSF,
- GSM7653243 PGE2_GM-CSF, Replicate1 PGE2_GM-CSF,
- GSM7653244 PGE2_GM-CSF, Replicate2 PGE2_GM-CSF,
- GSM7653245 LA_PGE2_GM-CSF, Replicate1 LA_PGE2_GM-CSF,
- GSM7653246 LA_PGE2_GM-CSF, Replicate2 LA_PGE2_GM-CSF,
- GSM7653247 4T1-tumor conditioned medium, Replicate1 4T1-tumor conditioned m…
- GSM7653248 4T1-tumor conditioned medium, Replicate2 4T1-tumor conditioned m…
- GSM7653249 sgNC, Replicate1 sgNC,
- GSM7653250 sgNC, Replicate2 sgNC,
- GSM7653251 sgAdar, Replicate1 sgAdar,
- GSM7653252 sgAdar, Replicate2 sgAdar,
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares tumor-associated, macrophages
- GSE282257 Mitochondria complex III-generated superoxide is essential for IL-10 secretion in macrophages 40 samples shares macrophages, complex
- 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
- GSE285794 Cancer cell-derived arginine fuels polyamine biosynthesis in tumor-associated macrophages to promote immune evasion 12 samples shares tumor-associated, macrophages
- GSE283089 MFRP in the retina is a molecular hub that organizes the apical membrane of RPE cells by engaging in interactions with specific protein and lipid molecules 12 samples shares interaction, specific
- GSE271267 Tumoral Interferon Beta Induces an Immune-Stimulatory Phenotype in Tumor-Associated Macrophages in Melanoma Brain Metastases 12 samples shares tumor-associated, macrophages
- GSE325061 Ubiquitylation by the GID/CTLH complex regulates the metabolic and innate immune response of macrophages to infection by Mycobacterium tuberculosis 12 samples shares macrophages, complex
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.