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Spatially restricted immune and microbiota-driven adaptation of the gut [Spatial Transcriptomics]

GSE245274 Mus musculus (mouse) Spatial transcriptomics 46 samples Submitted 2024/11/26 Platform GPL24247Platform GPL19057
At a glance

Spatial transcriptomics · mouse · 46 samples

What it is
Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism
Mus musculus (mouse)
Samples
46 samples: 15 conditions, mostly in triplicateGroups 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 restricted immune and microbiota-driven adaptation of the gutNature · 2024
Summary (written by the submitters)
The intestine is characterized by an environment where host requirements for efficient nutrient and water absorption are consequently paired with the requirement to establish and maintain tolerance to the outside environment. The organ is anatomically organized into the small intestine (SI) which specializes in nutrient absorption and the colon which specializes in water resorption.
Read the full summary ↓
The transcriptional and cellular circuits that define intestinal regionalization and their robustness, adaptability, and resilience to changes in the local environment are not well characterized. Here, we generated a comprehensive survey of the spatial and cellular landscape of the murine intestine to demonstrate the steady state transcriptional landscape of the murine intestine is robust, adaptable, and resilient to perturbation. We characterized the transcriptional landscape of the full length of the intestine and show it is established independently of the microbiota and is not under circadian regulation. In the colon, these regional circuits were characterized by unique subsets of structural cells. Moreover, we identified a spatial adaptation to the microbiota in the colon characterized by the emergence of unique structural cell subsets including an enterocyte, fibroblast, and goblet cell, with the later two co-occurring in space. Employing a model of acute spatiotemporal damage allowed us to show the spatial landscape and adaptations we identified are both resilient to inflammation. Our results demonstrate that intestinal circuits are under host control and spatial adaptations in the steady state as well as in the process of recovery from tissue damage in the inflamed state are primarily characterized by changes to structural cell types such as epithelial and stromal cells.
Published in
Spatially restricted immune and microbiota-driven adaptation of the gut
Mayassi T, Li C, Segerstolpe Å et al. · Nature 2024 · PMID 39567686 · doi:10.1038/s41586-024-08216-z
This dataset
Open GSE245274 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE245274_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

What the files usually look like: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1027702 and SRA study SRP466150. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39567686) ↗
Study design
15 conditions, mostly in triplicate
SPF Duodenum ×3 GF Duodenum ×3 SPF Jejunum 1 ×3 GF Jejunum 1 ×3 SPF Jejunum 2 ×3 GF Jejunum 2 ×3 SPF Ileum ×3 GF Ileum ×3 +13 more

Supports a between-group comparison across 40 samples.

How we read this: 15 replicated groups read from 46 sample titles; they account for 40 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.

Samples in this study

+ 6 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

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