Salmonella typhimurium targets distal colonocytes to trigger infection
Single-cell RNA-seq · mouse · 10 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 10 samples: 5 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
- Spatially resolved single-cell transcriptome analysis of murine Salmonella infection reveals the role of distal colonocytes in the inflammatory responseGut microbes · 2025
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 GSE291248_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1229626 and SRA study SRP566963. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8831668 colon_uninfected_d0_rep1 colon_uninfected_d0
- GSM8831669 colon_uninfected_d0_rep2 colon_uninfected_d0
- GSM8831670 colon_infected_d1_rep1 colon_infected_d1
- GSM8831671 colon_infected_d1_rep2 colon_infected_d1
- GSM8831672 colon_infected_d3_rep1 colon_infected_d3
- GSM8831673 colon_infected_d3_rep2 colon_infected_d3
- GSM8831674 colon_infected_d5_rep1 colon_infected_d5
- GSM8831675 colon_infected_d5_rep2 colon_infected_d5
- GSM8831676 colon_infected_d7_rep1 colon_infected_d7
- GSM8831677 colon_infected_d7_rep2 colon_infected_d7
- GSE290763 Salmonella typhimurium targets distal colonocytes to trigger infection [RNA-seq] 15 samples shares typhimurium, colonocytes, salmonella, targets, trigger, distal
- GSE250198 Loss of NR2F6 reduces tissue-resident macrophages and protects from Salmonella typhimurium infection 5 samples shares typhimurium, salmonella
- GSE278410 Salmonella infection accelerates potential maturation of the intestinal epithelium 32 samples shares salmonella
- GSE290553 How infection impacts regulation of adipocyte metabolism and does IFNγ directly targets adipocytes and mediates lipid metabolism in vivo following infection 16 samples shares targets
- GSE279651 scnasRNA-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection 12 samples shares salmonella
- GSE304820 Laurocapram inhibits Salmonella infection via dual mechanisms 12 samples shares salmonella
- GSE303403 Synergistic Multiple Effects of Resveratrol Combatting Salmonella Infection 12 samples shares salmonella
- GSE233489 scRNA-sequencing of colon and dura CD45+ cells following Salmonella infection 8 samples shares salmonella
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.