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Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle[RNA-Seq]

GSE247943 Mus musculus (mouse) RNA-seq (gene expression) 52 samples Submitted 2024/12/31 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 52 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
52 samples: 26 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)
Cell cycle (CC) is a fundamental biological process with robust, cyclical gene expression programs to facilitate cell division. In the immune system, a productive immune response requires the expansion of pathogen-responsive cell types, but whether CC also confers unique gene expression programs that inform the subsequent immunological response remains unclear.
Read the full summary ↓
Here we demonstrate that single macrophages adopt different plasticity states in CC which is a major source of heterogeneity in response to polarizing cytokines. Specifically, macrophage plasticity to interferon gamma (IFNG) is substantially reduced, while interleukin 4 (IL-4) can induce S-G2/M-biased gene expression. Additionally, IL-4 polarization shifts the CC-phase distribution of the population towards G2/M phase, providing a mechanism for reduced IFNG-induced repolarization. Finally, we show that macrophages express tissue remodeling genes in the S-G2/M-phases of CC, that can be also detected in vivo during muscle regeneration. Therefore, CC defines macrophage inflammatory and regenerative responses in a cyclical, CC-phase-dependent manner.
This dataset
Open GSE247943 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 GSE247943_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 PRJNA1040951 and SRA study SRP472277. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
26 conditions, mostly in duplicate
Bone marrow-derived macrophage-KO-CTR ×2 Bone marrow-derived macrophage-KO-IL4_rep24h ×2 Bone marrow-derived macrophage-KO-IL4+DEX ×2 Bone marrow-derived macrophage-KO-IL4+IFNG ×2 Bone marrow-derived macrophage-KO-IL4+IL10 ×2 Bone marrow-derived macrophage-KO-IL4+LPS ×2 Bone marrow-derived macrophage-KO-pIL4 ×2 Bone marrow-derived macrophage-KO-pIL4+DEX ×2 +18 more

Supports a between-group comparison across 52 samples.

How we read this: 26 replicated groups read from 52 sample titles; they account for 52 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

+ 12 more — browse all 52 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.