Bile acid receptor Tgr5 prevents macrophage hyperinflammation during bacterial sepsis through metabolic and epigenetic silencing
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.
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 GSE309415_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 PRJNA1336054 and SRA study SRP629402. 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.
- GSM9267061 WT1, Untreated control
- GSM9267062 WT1, Lm-stimulated
- GSM9267063 WT2, Untreated control
- GSM9267064 WT2, Lm-stimulated
- GSM9267065 WT3, Untreated control
- GSM9267066 WT3, Lm-stimulated
- GSM9267067 KO1, Untreated control
- GSM9267068 KO1, Lm-stimulated
- GSM9267069 KO2, Untreated control
- GSM9267070 KO2, Lm-stimulated
- GSM9267071 KO3, Untreated control
- GSM9267072 KO3, Lm-stimulated
- GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares epigenetic, silencing
- GSE250551 Targeting inflammation with chimeric antigen receptor macrophages using a signal switch 32 samples shares macrophage, receptor
- GSE99296 α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming 18 samples shares macrophage, epigenetic
- GSE272424 Rejuvenating endogenous antitumor immunity via a chimeric receptor-engineered oncolytic virus targeting tumor-associated macrophages 6 samples shares macrophage, receptor
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares macrophage, receptor
- GSE269191 ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vivo] 145 samples shares macrophage
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophage
- GSE276155 RBBP5 is an epigenetic regulator of mammalian hepatic 12h oscillator [RNA-seq] 96 samples shares epigenetic
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.