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Macrophages adopt mural cell function and marker expression for vascular support following ischemia

GSE211550 Mus musculus (mouse) Single-cell RNA-seq 1509 samples Submitted 2024/04/08 Platform GPL13112
At a glance

Single-cell RNA-seq · mouse · 1509 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
1509 samples: 17 conditions, mostly with about 24 replicates eachGroups 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
Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular supportNature cardiovascular research · 2024
Summary (written by the submitters)
We used scRNAseq to study if perivascular macrophages adopt a mural cell identity during tissue restoration in mouse models of ischemia
Published in
Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular support
Amoedo-Leite C, Parv K, Testini C et al. · Nature cardiovascular research 2024 · PMID 39196227 · doi:10.1038/s44161-024-00478-0
This dataset
Open GSE211550 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 GSE211550_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: 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 PRJNA870900 and SRA study SRP392886. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39196227) ↗
Study design
17 conditions, mostly with about 24 replicates each
mouse muscle ischemia d21 SS2_19_276_A ×24 mouse muscle ischemia d21 SS2_19_276_B ×24 mouse muscle ischemia d21 SS2_19_276_C ×24 mouse muscle ischemia d21 SS2_19_276_D ×24 mouse muscle ischemia d21 SS2_19_276_E ×24 mouse muscle ischemia d21 SS2_19_276_F ×24 mouse muscle ischemia d21 SS2_19_276_G ×24 mouse muscle ischemia d21 SS2_19_276_H ×24 +9 more

Supports a between-group comparison across 400 samples.

How we read this: 17 replicated groups read from the first 400 of 1509 sample titles; they account for 400 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

+ 1469 more — browse all 1509 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.