GEO series

TGF-b/Smad3 inhibition synergizes with PPARg agonism to reduce fibrosis and enhance functional beige adipogenesis

GSE268791 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/09/01 Platform 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 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.

Summary (written by the submitters)

Adipose tissue depots vary markedly in their ability to store and metabolize triglycerides, undergo beige adipogenesis and be susceptibile to metabolic disease. The molecular mechanisms that underlie such heterogeneity are not entirely clear. Previously, we showed that TGF-b signaling regulates the browning of white adipose tissue via recruitment of dedicated beige progenitors.

Read the full summary ↓

Here, we find that TGF-b signals dynamically regulate the balance between adipose tissue fibrosis and beige adipogenesis. Elevated basal and high-fat diet inducible activation of TGF-b/Smad3 signaling was observed in the visceral (epididymal) adipose tissue depot. Activation of TGF-b/Smad3 signaling was associated with increased adipose tissue fibrosis. RNA-seq combined with fluorescence-activated cell sorting of stromal vascular fraction of epididymal white adipose tissue depot resulted in identification of TGF-b/Smad3 regulated ITGA5+ fibrogenic progenitors. TGF-b/Smad3 signal inhibition, genetically or pharmacologically, reduced fibrosis and increased functional beige adipogenesis. TGF-b/Smad3 antagonized the beneficial effects of PPARγ , activation whereas TGF-b receptor 1 inhibition synergized with actions of rosiglitazone, a PPARγ agonist, to dampen fibrosis and promote beige adipogenesis. There was a positive correlation between TGF-b activation and levels of fibrosis marker, ITGA5, in human adipose tissue samples , with visceral (omental) adipose tissue depot exhibiting higher fibrosis potential than subcutaneous or brown adipose tissue depots. Taken together, out data provide TGF-b/Smad3 signaling operates at the nexus of adipose tissue fibrosis and functional beige adipogenesis.

This dataset

Open GSE268791 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 GSE268791_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 PRJNA1118757 and SRA study SRP511091. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

CD_mock ×3 CD_TGF-b ×3 CD_TGF-b/SB431542 ×3 HFD_mock ×3 Itga5-High_DM ×3 Itga5-Low_DM ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 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

GSM8299562 CD_mock_1 CD_mock
GSM8299563 CD_mock_2 CD_mock
GSM8299564 CD_mock_3 CD_mock
GSM8299565 CD_TGF-b_1 CD_TGF-b
GSM8299566 CD_TGF-b_2 CD_TGF-b
GSM8299567 CD_TGF-b_3 CD_TGF-b
GSM8299568 CD_TGF-b/SB431542_1 CD_TGF-b/SB431542
GSM8299569 CD_TGF-b/SB431542_2 CD_TGF-b/SB431542
GSM8299570 CD_TGF-b/SB431542_3 CD_TGF-b/SB431542
GSM8299571 HFD_mock_1 HFD_mock
GSM8299572 HFD_mock_2 HFD_mock
GSM8299573 HFD_mock_3 HFD_mock
GSM8299574 Itga5-High_DM_1 Itga5-High_DM
GSM8299575 Itga5-High_DM_2 Itga5-High_DM
GSM8299576 Itga5-High_DM_3 Itga5-High_DM
GSM8299577 Itga5-Low_DM1 Itga5-Low_DM
GSM8299578 Itga5-Low_DM2 Itga5-Low_DM
GSM8299579 Itga5-Low_DM3 Itga5-Low_DM

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