GEO series

PPARg T166 phosphorylation-mediated lipid synthesis sustains the reparative function of macrophages during tissue repair [RNA-seq]

GSE252899 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2024/07/30 Platform GPL34290Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 18 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: 18 samples: 6 × Skin Macrophages 6 dpi, WT, vs 6 × Skin Macrophages 6 dpi, TA, vs 3 × BMDMs, WT, RNA-seq vs 3 × BMDMs, TA, RNA-seqGroups 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: Lipid synthesis, triggered by PPARγ T166 dephosphorylation, sustains reparative function of macrophages during tissue repairNature communications · 2024

Summary (written by the submitters)

Macrophages exhibit a reparative phenotype that supports tissue repair and remodeling in response to tissue injury. However, the metabolic requirements that support this process have remained incompletely understood. Here, we showed that posttranslational modification (PTM) of peroxisome proliferator-activated receptor g (PPARg) regulated lipid synthesis in response to wound microenvironmental cues and that metabolic rewiring orchestrated the function of reparative macrophages.

Read the full summary ↓

In injured tissues, repair signaling attenuated macrophage PPARg threonine 166 (T166) phosphorylation, which induced a partially active PPARg program with increased binding activity to the regulator regions of lipid synthesis-associated genes, thereby activating lipogenesis. The accumulated lipids served as signaling molecules, triggering signal transducer and activator of transcription 3 (STAT3)-mediated growth factor expression, and supporting the synthesis of phospholipids for the expansion of the endoplasmic reticulum (ER), which is required for the secretion of proteins. Genetic or pharmacological inhibition of PPARg T166 phosphorylation promoted the reparative function of macrophages and facilitated tissue regeneration. In summary, we identified that PPARg T166-regulated lipid biosynthesis was essential for the anabolic demands of the activation and function of macrophages and provided a rationale for therapeutic targeting of tissue repair.

Published in

Lipid synthesis, triggered by PPARγ T166 dephosphorylation, sustains reparative function of macrophages during tissue repair

Zuo S, Wang Y, Bao H et al. · Nature communications 2024 · PMID 39179603 · doi:10.1038/s41467-024-51736-5

This dataset

Open GSE252899 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 GSE252899_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 PRJNA1063197 and SRA study SRP482896. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39179603) ↗

Study design

6 × Skin Macrophages 6 dpi, WT, vs 6 × Skin Macrophages 6 dpi, TA, vs 3 × BMDMs, WT, RNA-seq vs 3 × BMDMs, TA, RNA-seq

Supports a between-group comparison across 18 samples.

How we read this: 4 replicated groups read from 18 sample titles; they account for 18 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

GSM8010066 BMDMs, WT, RNA-seq rep1 BMDMs, WT, RNA-seq
GSM8010067 BMDMs, WT, RNA-seq rep2 BMDMs, WT, RNA-seq
GSM8010068 BMDMs, WT, RNA-seq rep3 BMDMs, WT, RNA-seq
GSM8010069 BMDMs, TA, RNA-seq rep1 BMDMs, TA, RNA-seq
GSM8010070 BMDMs, TA, RNA-seq rep2 BMDMs, TA, RNA-seq
GSM8010071 BMDMs, TA, RNA-seq rep3 BMDMs, TA, RNA-seq
GSM8328682 Skin Macrophages 6 dpi, WT, rep1 Skin Macrophages 6 dpi,…
GSM8328683 Skin Macrophages 6 dpi, WT, rep2 Skin Macrophages 6 dpi,…
GSM8328684 Skin Macrophages 6 dpi, WT, rep3 Skin Macrophages 6 dpi,…
GSM8328685 Skin Macrophages 6 dpi, WT, rep4 Skin Macrophages 6 dpi,…
GSM8328686 Skin Macrophages 6 dpi, WT, rep5 Skin Macrophages 6 dpi,…
GSM8328687 Skin Macrophages 6 dpi, WT, rep6 Skin Macrophages 6 dpi,…
GSM8328688 Skin Macrophages 6 dpi, TA, rep1 Skin Macrophages 6 dpi,…
GSM8328689 Skin Macrophages 6 dpi, TA, rep2 Skin Macrophages 6 dpi,…
GSM8328690 Skin Macrophages 6 dpi, TA, rep3 Skin Macrophages 6 dpi,…
GSM8328691 Skin Macrophages 6 dpi, TA, rep4 Skin Macrophages 6 dpi,…
GSM8328692 Skin Macrophages 6 dpi, TA, rep5 Skin Macrophages 6 dpi,…
GSM8328693 Skin Macrophages 6 dpi, TA, rep6 Skin Macrophages 6 dpi,…

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