GEO series

Clonorchis sinensis (C. sinensis) infection remodels the chromatin accessibility of hepatocellular carcinoma

GSE276855 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2024/11/26 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Topic: Hepatocellular carcinomaThis series is part of our curated briefing on it.
Samples: 16 samples: 16 samples, each with a distinct title — no replicated groupsGroups 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: Clonorchis sinensis infection remodels chromatin accessibility in hepatocellular carcinomaParasites & vectors · 2025

Summary (written by the submitters)

Background: Liver cancer is the third deadliest type of cancer, posing a serious threat to human health. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. C. sinensis, classified as a definite group I carcinogen by the IARC (International Agency for Research on Cancer), is an important risk factor for HCC.

Read the full summary ↓

Although many studies have shown that C. sinensis infection affects the prognosis of HCC patients, the specific mechanisms are still unclear, especially the dynamics and regulatory roles of chromatin accessibility. Results: In this study, we integrated ATAC-seq, RNA-seq, and ChIP-seq data to elucidate changes in the epigenetics of HCC after the C. sinensis infection. Many different accessibility regions (DARs) were identified both in tumors and adjacent tissue after the C. sinensis infection. Meanwhile, top TFs whose motifs were enriched in DAR were found, such as HNF4a, FOXI1, etc. Although there were slight deviations, epigenetic changes were found to be consistent with gene expression levels. We also revealed that H3K9ac, H3K4me2, H3K4me3, H3K27ac, and H3K4me1 were associated with chromatin accessibility. Importantly, we also found potential evidence that C. sinensis infection would alter the spatial structure of the HCC genome. Finally, both molecular experimental results and clinical data certified that C. sinensis infection would promote the metastasis of HCC. Conclusions: C. sinensis infection will remodel the chromatin accessibility of HCC, leading to changes in gene expression levels. This study provides conclusive evidence that C. sinensis infection alters the epigenetics of HCC.

Published in

Clonorchis sinensis infection remodels chromatin accessibility in hepatocellular carcinoma

Yang W, Wei C, Chen J et al. · Parasites & vectors 2025 · PMID 40640964 · doi:10.1186/s13071-025-06909-6

This dataset

Open GSE276855 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Hepatocellular carcinoma landscape →

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 GSE276855_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1159298 and SRA study SRP531886. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40640964) ↗

Study design

16 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 16 sample titles: 16 distinct titles with little repetition. 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

GSM8506982 HCC,Cs-,1,P
GSM8506983 HCC,Cs-,1,T
GSM8506984 HCC,Cs-,2,P
GSM8506985 HCC,Cs-,2,T
GSM8506986 HCC,Cs-,3,P
GSM8506987 HCC,Cs-,3,T
GSM8506988 HCC,Cs-,4,P
GSM8506989 HCC,Cs-,4,T
GSM8506990 HCC,Cs+,1,P
GSM8506991 HCC,Cs+,1,T
GSM8506992 HCC,Cs+,2,P
GSM8506993 HCC,Cs+,2,T
GSM8506994 HCC,Cs+,3,P
GSM8506995 HCC,Cs+,3,T
GSM8506996 HCC,Cs+,4,P
GSM8506997 HCC,Cs+,4,T

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GSE109211 Molecular predictors of prevention of recurrence in hepatocellular carcinoma with sorafenib as adjuvant treatment in the phase 3 STORM trial 140 samples same disease briefing · shares hepatocellular
GSE10186 Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma 118 samples same disease briefing · shares hepatocellular
GSE105130 Comprehensive analysis of Transcriptome Profiles in Hepatocellular Carcinoma patients 52 samples same disease briefing · shares hepatocellular
GSE140228 Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma 41 samples same disease briefing · shares hepatocellular
GSE114564 Identification of novel serum biomarkers in early-stage HCC patients. 118 samples same disease briefing

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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