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Transcriptomic profile of monocytes/ macrophages from injured bone, muscle, skin or heart tissues of Treg-depleted mice

GSE268828 Mus musculus (mouse) RNA-seq (gene expression) 56 samples Submitted 2024/05/31 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 56 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
56 samples: 16 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
Tregs delivered post-myocardial infarction adopt an injury-specific phenotype promoting cardiac repair via macrophages in miceNature communications · 2024
Summary (written by the submitters)
Mice were depleted of Tregs, and bone, muscle, skin or heart injuries were performed. On day 4 and 7 post-injury, the tissues were harvested and the endogenous monocytes/macrophages were sorted using FACS. These were then used for bulk RNA sequencing, to compare the transcriptomic profiles of injured tissue monocytes/ macrophages in Treg-depleted mice versus control mice post-injury.
Published in
Tregs delivered post-myocardial infarction adopt an injury-specific phenotype promoting cardiac repair via macrophages in mice
Alshoubaki YK, Nayer B, Lu YZ et al. · Nature communications 2024 · PMID 39090108 · doi:10.1038/s41467-024-50806-y
This dataset
Open GSE268828 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 GSE268828_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1118806 and SRA study SRP511100. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39090108) ↗
Study design
16 conditions, mostly in triplicate
Bone_Treg_depleted_D7 ×5 Bone_Control_D7 ×5 Skin_Treg_depleted_D4 ×4 Skin_Control_D4 ×4 Skin_Treg_depleted_D7 ×4 Skin_Control_D7 ×4 MI_Heart_Treg_depleted_D7 ×3 MI_Heart_Control_D7 ×3 +8 more

Supports a between-group comparison across 56 samples.

How we read this: 16 replicated groups read from 56 sample titles; they account for 56 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

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.