Senescent stroma mediates immunosuppression and drives breast cancer progression [CAF]
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 12 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
- Senescent CAFs Mediate Immunosuppression and Drive Breast Cancer ProgressionCancer discovery · 2024
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 GSE229350_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 PRJNA954044 and SRA study SRP431852. 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 12 sample titles: 12 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.
- GSM7159148 27_icaf
- GSM7159149 27_m2cafneg
- GSM7159150 27_m2cafpos
- GSM7159151 27_vacf
- GSM7159152 30_icaf
- GSM7159153 30_m2cafneg
- GSM7159154 30_m2cafpos
- GSM7159155 30_vcaf
- GSM7159156 31_icaf
- GSM7159157 31_m2cafneg
- GSM7159158 31_m2cafpos
- GSM7159159 31_vcaf
- GSE294999 Obesity-driven inflammation enables triple-negative breast cancer progression through immunosuppression [scRNA-Seq] 16 samples shares immunosuppression, progression, breast
- GSE241770 ACSS2 mediates an epigenetic pathway to regulate maternal Beta-cell adaptation and progression of gestational diabetes (scRNA-Seq) 7899 samples shares progression, mediates
- GSE263963 The temporal progression of lung immune remodeling during breast cancer metastasis 38 samples shares progression, breast
- GSE231802 IL-1R signaling drives enteric glia-macrophage interaction in colorectal cancer progression [bulkRNA-Seq] 36 samples shares progression, drives
- GSE325774 WDR82 suppresses breast cancer progression by inhibiting ERK-driven chemokine expression and neutrophil infiltration 9 samples shares progression, breast
- GSE341921 PGK1 moonlights as an NF-kB/p65 kinase to orchestrate M2-like macrophage-mediated immunosuppression in triple-negative breast cancer 6 samples shares immunosuppression, breast
- GSE261780 Iron oxide nanoparticles inhibit tumor progression and suppress lung metastases in mouse models of breast cancer 72 samples shares progression, breast
- GSE289885 Hybrid hydrogel–extracellular matrix scaffolds identify biochemical and mechanical signatures of cardiac ageing 29 samples shares caf
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.