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Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia [scRNA-seq]

GSE263545 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2024/04/14 Platform GPL18480

At a glance

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.
Organism: Mus musculus (mouse)
Samples: 10 samples: 3 × Baseline, Csf1r∆FIRE/+, FIRE_NI_CTRL vs 2 × MI d2, Csf1r∆FIRE/∆FIRE, FIRE_IF_KO vs 2 × MI d2, Csf1r∆FIRE/+, FIRE_IF_WT vs 2 × Baseline, Csf1r∆FIRE/∆FIRE, FIRE_NI_KOGroups 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: Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemiaeLife · 2024

Summary (written by the submitters)

Cardiac macrophages are heterogenous in phenotype and functions, which has been associated with differences in their ontogeny. Despite extensive research, our understanding of the precise role of different subsets of macrophages in ischemia/reperfusion injury remains incomplete. We here investigated macrophage lineages and ablated tissue macrophages in homeostasis and after I/R injury in a CSF1R-dependent manner.

Read the full summary ↓

Genomic deletion of a fms-intronic regulatory element (FIRE) in the Csf1r locus resulted in specific absence of resident homeostatic and antigen-presenting macrophages, without affecting the recruitment of monocyte-derived macrophages to the infarcted heart. Specific absence of homeostatic, monocyte-independent macrophages altered the immune cell crosstalk in response to injury and induced proinflammatory neutrophil polarization, resulting in impaired cardiac remodelling without influencing infarct size. In contrast, continuous CSF1R inhibition led to depletion of both resident and recruited macrophage populations. This augmented adverse remodelling after I/R and led to an increased infarct size and deterioration of cardiac function. In summary, resident macrophages orchestrate inflammatory responses improving cardiac remodelling, while recruited macrophages determine infarct size after I/R injury. These findings attribute distinct beneficial effects to different macrophage populations in the context of myocardial infarction.

Published in

Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia

Weinberger T, Denise M, Joppich M et al. · eLife 2024 · PMID 38775664 · doi:10.7554/eLife.89377

This dataset

Open GSE263545 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 GSE263545_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 PRJNA1098025 and SRA study SRP500528. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38775664) ↗

Study design

3 × Baseline, Csf1r∆FIRE/+, FIRE_NI_CTRL vs 2 × MI d2, Csf1r∆FIRE/∆FIRE, FIRE_IF_KO vs 2 × MI d2, Csf1r∆FIRE/+, FIRE_IF_WT vs 2 × Baseline, Csf1r∆FIRE/∆FIRE, FIRE_NI_KO

Supports a between-group comparison across 9 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 9 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

GSM8194262 MI d2, Csf1r∆FIRE/∆FIRE, FIRE_IF_KO R1 MI d2, Csf1r∆FIRE/∆FIRE…
GSM8194263 MI d2, Csf1r∆FIRE/∆FIRE, FIRE_IF_KO R2 MI d2, Csf1r∆FIRE/∆FIRE…
GSM8194264 MI d2, Csf1r∆FIRE/+, FIRE_IF_WT R1 MI d2, Csf1r∆FIRE/+, FI…
GSM8194265 MI d2, Csf1r∆FIRE/+, FIRE_IF_WT R2 MI d2, Csf1r∆FIRE/+, FI…
GSM8194266 Baseline, Csf1r∆FIRE/+, FIRE_NI_CTRL R1 Baseline, Csf1r∆FIRE/+,…
GSM8194267 Baseline, Csf1r∆FIRE/+, FIRE_NI_CTRL R2 Baseline, Csf1r∆FIRE/+,…
GSM8194268 Baseline, Csf1r∆FIRE/+, FIRE_NI_CTRL R3 Baseline, Csf1r∆FIRE/+,…
GSM8194269 Baseline, Csf1r∆FIRE/∆FIRE , FIRE_NI_KO R1
GSM8194270 Baseline, Csf1r∆FIRE/∆FIRE, FIRE_NI_KO R2 Baseline, Csf1r∆FIRE/∆F…
GSM8194271 Baseline, Csf1r∆FIRE/∆FIRE, FIRE_NI_KO R3 Baseline, Csf1r∆FIRE/∆F…

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