Spatially restricted immune and microbiota-driven adaptation of the gut [scRNA-seq]
Single-cell RNA-seq · mouse · 26 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 26 samples: 26 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.
- Paper
- Spatially restricted immune and microbiota-driven adaptation of the gutNature · 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 GSE245315_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 PRJNA1027816 and SRA study SRP466212. 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 26 sample titles: 26 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.
- GSM7840733 M001A
- GSM7840734 M001B
- GSM7840735 M001C
- GSM7840736 M001D
- GSM7840737 M002A
- GSM7840738 M002B
- GSM7840739 M002D
- GSM7840740 M003A
- GSM7840741 M003B
- GSM7840742 M003C
- GSM7840743 M003D
- GSM7840744 M004A
- GSM7840745 M004B
- GSM7840746 M004C
- GSM7840747 M004D
- GSM7840748 M005A
- GSM7840749 M005B
- GSM7840750 M005C
- GSM7840751 M005D
- GSM7840752 M006A
- GSM7840753 M006B
- GSM7840754 M006C
- GSM7840755 M006D
- GSM7840756 M007B
- GSM7840757 M007C
- GSM7840758 M008C
- GSE245316 Spatially restricted immune and microbiota-driven adaptation of the gut 72 samples shares microbiota-driven, restricted, adaptation, spatially
- GSE245274 Spatially restricted immune and microbiota-driven adaptation of the gut [Spatial Transcriptomics] 46 samples shares microbiota-driven, restricted, adaptation, spatially
- GSE241770 ACSS2 mediates an epigenetic pathway to regulate maternal Beta-cell adaptation and progression of gestational diabetes (scRNA-Seq) 7899 samples shares adaptation, scrna-seq
- GSE215960 Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma [scRNA-seq] 192 samples shares adaptation, scrna-seq
- GSE280514 Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair. 48 samples shares restricted, spatially
- GSE268876 Spatially clustered type I interferon responses at injury borderzones [scRNA-Seq] 12 samples shares spatially, scrna-seq
- GSE327449 Heterogeneity in hematopoietic stem cell enables adaptation to the aged microenvironment [scRNA-seq] 12 samples shares adaptation, scrna-seq
- GSE280652 Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair. 42 samples shares restricted, spatially
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.