GEO series

Maintenance of histone crotonylation by YEATS2 and GCDH drives EMT in head and neck cancer [ChIP-seq]

GSE275975 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2025/07/15 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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: Head and neck cancerThis series is part of our curated briefing on it.
Samples: 10 samples: 2 × BICR10_YEATS2 vs 2 × BICR10_Input vs 2 × BICR10_shControl_H3K27C vs 2 × BICR10_shYEATS2_H3K27CGroups 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: Interplay of YEATS2 and GCDH regulates histone crotonylation and drives EMT in head and neck cancereLife · 2025

Summary (written by the submitters)

Regulation of gene expression is an integral cellular process, fine-tuned by epigenetic marks like histone modifications. Perturbations in the activity or abundance of epigenetic factors can lead, or contribute to tumorigenesis in healthy cells. Remarkably, the addition of epigenetic marks is dependent on the metabolites produced during several essential cellular pathways.

Read the full summary ↓

Here, we have explored the interplay between a highly expressed epigenetic factor YEATS2, and a metabolic enzyme GCDH in regulating epithelial to mesenchymal transition in head and neck cancer. We report the results of RNA-seq in YEATS2-silenced BICR10 cells to investigate the effect of YEATS2 in influencing gene expression globally. We have also performed ChIP-seq using YEATS2 antibody in BICR10 cells to obtain the globally occupied sites of YEATS2. Lastly, we report the changes in crotonylation at histone 3 lysine 27 (H3K27Cr) upon YEATS2 downregulation in BICR10 by performing ChIP-seq in shControl vs. shYEATS2 cells.

Published in

Interplay of YEATS2 and GCDH regulates histone crotonylation and drives EMT in head and neck cancer

Pant D, Kakani P, Joshi R et al. · eLife 2025 · PMID 40810390 · doi:10.7554/eLife.103321

This dataset

Open GSE275975 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Head and neck cancer 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 GSE275975_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 PRJNA1154002 and SRA study SRP529419. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40810390) ↗

Study design

2 × BICR10_YEATS2 vs 2 × BICR10_Input vs 2 × BICR10_shControl_H3K27C vs 2 × BICR10_shYEATS2_H3K27C

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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

GSM8488889 BICR10_YEATS2_1 BICR10_YEATS2
GSM8488890 BICR10_YEATS2_2 BICR10_YEATS2
GSM8488891 BICR10_Input_1 BICR10_Input
GSM8488892 BICR10_Input_2 BICR10_Input
GSM8488893 BICR10_shControl_H3K27Cr_1 BICR10_shControl_H3K27C
GSM8488894 BICR10_shControl_H3K27Cr_2 BICR10_shControl_H3K27C
GSM8488895 BICR10_shYEATS2_H3K27Cr_1 BICR10_shYEATS2_H3K27C
GSM8488896 BICR10_shYEATS2_H3K27Cr_2 BICR10_shYEATS2_H3K27C
GSM8488897 BICR10_shControl_Input
GSM8488898 BICR10_shYEATS2_Input

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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.