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ChIP-seq and CUT&Tag profiling of the genome binding of YAP/TAZ-TEAD and SMAD3 in the human HCC cell line HCCLM3 [CUT&Tag]

GSE330469 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2026/05/16 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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
24 samples: 12 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)
This study generated ChIP-seq and CUT&Tag datasets to profile genome-wide occupancy of YAP, TAZ, TEAD1, SMAD3, and VGLL4 in the human hepatocellular carcinoma cell line HCCLM3. Profiling was performed under four conditions: untreated control, TGF-beta1 stimulation (2.5 ng/ml for 2 h), siRNA-mediated knockdown of YAP and TAZ followed by TGF-beta1 stimulation (2.5 ng/ml for 2 h), and stable KLF2 overexpression followed by TGF-beta1 stimulation (2.5 ng/ml for 2 h).
Read the full summary ↓
ChIP-seq was also used to profile the histone modifications H3K27ac, H3K4me1, H3K4me3, and H3K18la. These datasets provide a resource for studying transcription factor binding and chromatin states in HCCLM3 cells.
This dataset
Open GSE330469 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 GSE330469_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 PRJNA1464454 and SRA study SRP699211. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in duplicate
IgG, CUT&Tag, ×2 Control, SMAD3, CUT&Tag, ×2 Control, TEAD1, CUT&Tag, ×2 Control, VGLL4, CUT&Tag, ×2 TGFb1, SMAD3, CUT&Tag, ×2 TGFb1, TEAD1, CUT&Tag, ×2 TGFb1, VGLL4, CUT&Tag, ×2 siYAP/TAZ, TGFb1, SMAD3, CUT&Tag, ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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
More Hepatocellular carcinoma datasets

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

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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.