Deletion of sphingosine 1-phosphate receptor 1 in myeloid cells reduces hepatic inflammatory macrophages and attenuates MASH
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 GSE288368_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 PRJNA1217035 and SRA study SRP560636. 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.
- GSM8766414 1 - WT CD 2
- GSM8766415 2 - WT CD 3
- GSM8766416 3 - WT CD 4
- GSM8766417 4 - KO CD 1
- GSM8766418 5- KO CD 2
- GSM8766419 6 - KO CD 3
- GSM8766420 7 - WT FFC 2
- GSM8766421 8 - WT FFC 3
- GSM8766422 9 - WT FFC 4
- GSM8766423 13 - KO FFC 1
- GSM8766424 14 - KO FFC 4
- GSM8766425 15 - KO FFC 7
- GSE266438 Loss of Sphingosine-1-Phosphate Receptor 4 weakens innate mechanisms leading to defective lymph node hypertrophy and germinal center formation 45 samples shares sphingosine, 1-phosphate, receptor
- GSE264083 Mycobacterium abscessus infection in fetal liver derived alveolar-like macrophages activates distinct inflammatory responses compared to myeloid-derived macrophages 36 samples shares macrophages, myeloid
- GSE250551 Targeting inflammation with chimeric antigen receptor macrophages using a signal switch 32 samples shares macrophages, receptor
- GSE325918 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [RNA-seq] 32 samples shares macrophages, receptor
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares macrophages, deletion
- GSE272424 Rejuvenating endogenous antitumor immunity via a chimeric receptor-engineered oncolytic virus targeting tumor-associated macrophages 6 samples shares macrophages, 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 macrophages, receptor
- GSE316023 AI digital pathology as a key tool providing in-depth understanding of the progression and regression of MASH and fibrosis in male mouse models 77 samples shares mash
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.