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ER-resident CCDC134 safeguards TLR4 maturation by maintaining gp96 stability

GSE297380 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/08/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 8 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.
Paper
ER-resident CCDC134 safeguards TLR4 maturation by maintaining gp96 stabilityProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
Toll-like receptor 4 (TLR4), a pattern-recognition receptor located on the plasma membrane, senses extracellular danger signals to initiate inflammatory immune responses. It is initially synthesized in the endoplasmic reticulum (ER), undergoes N-linked glycosylation, and is subsequently transported to the Golgi before ultimately reaching the plasma membrane.
Read the full summary ↓
However, the mechanisms underlying the processing and maturation of TLR4 in the ER remain elusive. Through whole genome-wide CRISPR screening, CCDC134 was identified as a critical and essential factor for TLR4-dependent inflammatory response. Localization of CCDC134 in the ER lumen rather than its exosome-mediated secretion is required for its role in TLR4 signaling. Loss of CCDC134 results in the retention of TLR4 in the ER for subsequent ER-associated degradation, and thus blockade of TLR4 maturation and plasma membrane trafficking. Defects in TLR4 processing and maturation in the ER in CCDC134-depleted cells are caused by aberrant hyperglycosylation and destabilization of glycoprotein 96 (gp96), a key chaperone of TLR4. These results suggest that CCDC134 controls gp96 glycosylation to facilitate TLR4 maturation in the ER.
Published in
ER-resident CCDC134 safeguards TLR4 maturation by maintaining gp96 stability
Bai Y, Zhang C, Liu H et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40828012 · doi:10.1073/pnas.2512154122
This dataset
Open GSE297380 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 GSE297380_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 PRJNA1263720 and SRA study SRP585860. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40828012) ↗
Study design
8 conditions, mostly in duplicate
iBMDM cells, WT-1 repeat ×2 iBMDM cells, WT-2 repeat ×2 iBMDM cells, CCDC134KO-1 repeat ×2 iBMDM cells, CCDC134KO-2 repeat ×2 iBMDM cells, WT-1-LPS repeat ×2 iBMDM cells, WT-2-LPS repeat ×2 iBMDM cells, CCDC134KO-1-LPS repeat ×2 iBMDM cells, CCDC134KO-2-LPS repeat ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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
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