GEO series

Transglutaminase 2 regulates vimentin-dependent proteostasis during macrophage activation in sepsis

GSE301229 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2026/01/29 Platform GPL28457Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 21 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: 21 samples: 7 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)

Sepsis-associated liver dysfunction (SALD) is a life-threatening condition with a high mortality rate and no mechanism-based therapy. In this study, we identified transglutaminase 2 (TG2) as a druggable driver of macrophage-mediated liver inflammation in murine lipopolysaccharide (LPS)-induced sepsis. Pharmacological inhibition of TG2 significantly improved survival and reduced multi-organ inflammation, with the liver as a primary therapeutic target.

Read the full summary ↓

Mechanistically, TG2 activity was upregulated in macrophages, where it cross-linked vimentin to promote oligomerization and intermediate filament remodeling. Genetic ablation of TG2 or vimentin suppressed macrophage cytokine production and attenuated LPS-induced inflammation. Notably, vimentin-deficient macrophages exhibited enhanced proteasome recruitment to detergent-insoluble protein aggregates, accelerating the degradation of proinflammatory mediators such as TRAF6, thereby dampening NF-κB signaling. Proteomic profiling revealed a previously unrecognized Rab27a-positive vesicle trafficking pathway for inflammatory aggregate clearance. Together, these findings define a TG2–vimentin axis that controls macrophage activation through proteostasis regulation, linking cytoskeletal remodeling to inflammatory signaling. Our study suggests that targeting this axis, either via TG2 inhibition or modulation of vimentin-dependent proteostasis, represents a novel therapeutic strategy for the treatment of SALD.

This dataset

Open GSE301229 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 GSE301229_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 PRJNA1284302 and SRA study SRP597828. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

7 conditions, mostly in duplicate

WT RAW264.7 cells, PBS, 24 h, ×2 WT RAW264.7 cells, 1 µg/mL LPS, 24 h, ×2 WT RAW264.7 cells, 1 µg/mL LPS plus 0.5 mM CT… ×2 WT RAW264.7 cells, PBS, 12 h, ×2 WT RAW264.7 cells, 1 µg/mL LPS, 12 h, ×2 Vim-KO RAW264.7 cells, PBS, 12 h, ×2 Vim-KO RAW264.7 cells, 1 µg/mL LPS, 12 h, ×2 WT C57BL/6J, PBS i.p ×1 +6 more

Supports a between-group comparison across 14 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 14 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

GSM9078340 WT C57BL/6J, PBS i.p.
GSM9078341 WT C57BL/6J, 30 mg/kg LPS i.p.
GSM9078342 WT C57BL/6J, 30 mg/kg LPS plus 100mg/kg CTM i.p.
GSM9078343 WT C57BL/6J (no liver macrophage depletion), LPS i.p.
GSM9078344 WT C57BL/6J (liver macrophage depletion), LPS i.p.
GSM9078345 TG2-KO C57BL/6J, PBS i.p.
GSM9078346 TG2-KO C57BL/6J, 30 mg/kg LPS i.p.
GSM9078347 WT RAW264.7 cells, PBS, 24 h, rep1 WT RAW264.7 cells, PBS,…
GSM9078348 WT RAW264.7 cells, PBS, 24 h, rep2 WT RAW264.7 cells, PBS,…
GSM9078349 WT RAW264.7 cells, 1 µg/mL LPS, 24 h, rep1 WT RAW264.7 cells, 1 µg…
GSM9078350 WT RAW264.7 cells, 1 µg/mL LPS, 24 h, rep2 WT RAW264.7 cells, 1 µg…
GSM9078351 WT RAW264.7 cells, 1 µg/mL LPS plus 0.5 mM CTM, 24 h, rep1 WT RAW264.7 cells, 1 µg…
GSM9078352 WT RAW264.7 cells, 1 µg/mL LPS plus 0.5 mM CTM, 24 h, rep2 WT RAW264.7 cells, 1 µg…
GSM9078353 WT RAW264.7 cells, PBS, 12 h, rep1 WT RAW264.7 cells, PBS,…
GSM9078354 WT RAW264.7 cells, PBS, 12 h, rep2 WT RAW264.7 cells, PBS,…
GSM9078355 WT RAW264.7 cells, 1 µg/mL LPS, 12 h, rep1 WT RAW264.7 cells, 1 µg…
GSM9078356 WT RAW264.7 cells, 1 µg/mL LPS, 12 h, rep2 WT RAW264.7 cells, 1 µg…
GSM9078357 Vim-KO RAW264.7 cells, PBS, 12 h, rep1 Vim-KO RAW264.7 cells, …
GSM9078358 Vim-KO RAW264.7 cells, PBS, 12 h, rep2 Vim-KO RAW264.7 cells, …
GSM9078359 Vim-KO RAW264.7 cells, 1 µg/mL LPS, 12 h, rep1 Vim-KO RAW264.7 cells, …
GSM9078360 Vim-KO RAW264.7 cells, 1 µg/mL LPS, 12 h, rep2 Vim-KO RAW264.7 cells, …

Datasets on a similar topic

GSE309415 Bile acid receptor Tgr5 prevents macrophage hyperinflammation during bacterial sepsis through metabolic and epigenetic silencing 12 samples shares macrophage, sepsis
GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares macrophage, activation
GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares macrophage, activation
GSE99296 α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming 18 samples shares macrophage, activation
GSE245646 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ATAC-seq_muscle] 22 samples shares macrophage, activation
GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares macrophage
GSE337952 Transcriptomic Profiling of Murine Macrophages During Francisella tularensis Infection 20 samples shares macrophage
GSE269191 ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vivo] 145 samples shares macrophage

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.