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A Pathogenic CD8⁺ TRM–Chemokine Axis Orchestrates Liver Fibrosis and Provides Circulating Biomarkers during Chronic Clonorchis sinensis Infection

GSE302945 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/06/09 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: 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)
Clonorchis sinensis, a carcinogenic hepatobiliary trematode, drives severe pathological sequelae in humans. However, the immunological mechanisms underlying its chronic persistence remain incompletely elucidated. We systematically characterized the spatiotemporal dynamics of host immune responses during long-term C. sinensis infection.
Read the full summary ↓
Systemically, immunity evolved from an early mixed Th1/Th2/Th17 response toward eventual immune resolution. In contrast, hepatic immunity shifted from an initial Th2 bias to sustained pro-inflammatory activation, paralleling progressive liver pathology. Mechanistically, this hepatic immunopathology was driven by the expansion of CD8⁺ tissue-resident memory T (TRM) cells, which secreted high levels of CCL3, CCL4, CCL5, granzyme B, and granzyme K. Functional analyses demonstrated that CD8⁺ TRM cells orchestrated immune cell recruitment and fibroblast activation, with CD8⁺ T cell depletion significantly ameliorating liver damage. Notably, CCL4 was predominantly produced by CD8⁺ TRM cells and its serum levels correlated with hepatic pathology in both murine models and human patients with clonorchiasis. Our findings identify CD8⁺ TRM cells and CCL-mediated signaling as key drivers of chronic C. sinensis-induced liver immunopathology, highlighting promising targets for therapeutic intervention.
This dataset
Open GSE302945 in finder → Find more mouse 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 GSE302945_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 PRJNA1292873 and SRA study SRP601620. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
NPCs, liver, uninfected, GEX, ×3 NPCs, liver, C.sinensis 6 wpi, GEX, ×3 NPCs, liver, uninfected, TCR, ×3 NPCs, liver, C.sinensis 6 wpi, TCR, ×3 NPCs, liver, C.sinensis 16 wpi, GEX, ×2 NPCs, liver, C.sinensis 16 wpi, TCR, ×2

Supports a between-group comparison across 16 samples.

How we read this: 6 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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