Tissue niche influences immune and metabolic profiles to Staphylococcus aureus biofilm
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: 3 × Craniotomy TNF KO mice vs 3 × Craniotomy WT mice vs 3 × PJI TNF KO mice vs 3 × PJI WT miceGroups 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
- Tissue niche influences immune and metabolic profiles to Staphylococcus aureus biofilm infectionNature communications · 2024
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 GSE252481_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 PRJNA1060714 and SRA study SRP481149. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8001962 Craniotomy TNF KO mice 1 Craniotomy TNF KO mice
- GSM8001963 Craniotomy TNF KO mice 2 Craniotomy TNF KO mice
- GSM8001964 Craniotomy TNF KO mice 3 Craniotomy TNF KO mice
- GSM8001965 Craniotomy WT mice 1 Craniotomy WT mice
- GSM8001966 Craniotomy WT mice 2 Craniotomy WT mice
- GSM8001967 Craniotomy WT mice 3 Craniotomy WT mice
- GSM8001968 PJI TNF KO mice 1 PJI TNF KO mice
- GSM8001969 PJI TNF KO mice 2 PJI TNF KO mice
- GSM8001970 PJI TNF KO mice 3 PJI TNF KO mice
- GSM8001971 PJI WT mice 1 PJI WT mice
- GSM8001972 PJI WT mice 2 PJI WT mice
- GSM8001973 PJI WT mice 3 PJI WT mice
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- GSE271290 The effects of Erastin on the proliferation of Staphylococcus aureus in mouse macrophages 12 samples shares staphylococcus, aureus
- GSE248222 Impact of Maternal Immune Activation and Sex on Placental and Fetal Brain Cytokine and Gene Expression Profiles in a Preclinical Model of Neurodevelopmental Disorders 64 samples shares profiles
- GSE279351 Liver-specific inactivation of Cideb improves metabolic profiles and ameliorates steatohepatitis and fibrosis in animal models for MASH 45 samples shares profiles
- GSE310501 Mesothelioma location influences the tumour microenvironment and immune checkpoint therapy response in preclinical models 31 samples shares influences
- GSE262540 Myelin oligodendrocyte glycoprotein reactive Th17 cells drive Janus Kinase 1 dependent transcriptional reprogramming in astrocytes and alter cell surface cytokine receptor profiles during experimental autoimmune encephalomyelitis. 12 samples shares profiles
- GSE241165 Characterizing the gene expression profiles of 4T1 and 4T1.2 cells at different stages of bone metastsis using SMART-Seq2 technology 1248 samples shares profiles
- GSE201417 Gene expression profiles of cardiac neural crest cells during heart development 294 samples shares profiles
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.