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Transcriptomic profiling of macrophages that phagocytosed apoptotic Treg or conventional CD4⁺ T (Tconv) cells under different polarization conditions [RNA-Seq]

GSE325329 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2026/05/15 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 11 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
Macrophage efferocytosis plays a central role in the regulation of inflammation and tissue homeostasis. Regulatory T (Treg) cells are known to influence macrophage function, but the impact of macrophage phagocytosis of apoptotic Treg cells on macrophage polarization remains poorly understood. In this study, bone marrow–derived macrophages (BMDMs) were co-cultured with apoptotic Treg cells or conventional CD4⁺ T (Tconv) cells.
Read the full summary ↓
Apoptosis of T cells was induced by ATP/NAD⁺ treatment, and CD27 downregulation was used as an indicator of sensitivity to ATP/NAD⁺-mediated cell death. Treg and Tconv cells were labeled with anti-CD4 antibodies conjugated to BV421 or Alexa647 to enable detection of phagocytosis. BMDMs and apoptotic T cells were co-cultured under three conditions: non-polarizing conditions, IFN-γ stimulation, or IL-10 stimulation. After 48 hours of co-culture, macrophages were sorted based on phagocytosis status into three populations: macrophages that had phagocytosed Treg cells, macrophages that had phagocytosed Tconv cells, and macrophages that had not phagocytosed T cells. RNA sequencing was then performed to characterize transcriptional changes associated with phagocytosis of different T cell subsets and polarization conditions.
This dataset
Open GSE325329 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 GSE325329_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 PRJNA1439728 and SRA study SRP685029. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
11 conditions, mostly in duplicate
BMDMs cultured for 48 h in non-polarizing con… ×4 BMDMs polarized wih IFNg for 48 h, non-phagoc… ×4 BMDMs polarized wih IL-10 for 48 h, non-phago… ×4 BMDMs polarized wih IFNg for 48 h, BV421-labe… ×2 BMDMs polarized wih IFNg for 48 h, Ax647-labe… ×2 BMDMs polarized wih IFNg for 48 h, Ax647-labe… ×2 BMDMs polarized wih IFNg for 48 h, BV421-labe… ×2 BMDMs polarized wih IL-10 for 48 h, BV421-lab… ×2 +3 more

Supports a between-group comparison across 28 samples.

How we read this: 11 replicated groups read from 28 sample titles; they account for 28 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
Datasets on a similar topic

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