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HDAC5 Depletion Promotes Hyper-Acetylation of FOXA1 and Potentiating HIF1α Transcriptional Activation in Pancreatic Cancer

GSE263573 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 32 samples Submitted 2026/02/28 Platform GPL11154
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 32 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
Pancreatic cancerThis series is part of our curated briefing on it.
Samples
32 samples: 14 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)
Unlike class I Histone deacetylase (HDAC) members (HDAC1, 2, 3, etc.), HDAC5, a class IIa HDAC member, is downregulated in multiple solid tumors, including pancreatic cancer, and its loss is associated with unfavorable prognosis. We observed that HDAC5 mediates FOXA1-K270 deacetylation and represses HIF1? signaling via FOXA1. To further validate our hypothesis, we performed the ChIP-seq of relevant proteins in our working model to determine HDAC5?s impact on FOXA1-HIF1? signaling.
This dataset
Open GSE263573 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Pancreatic 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 GSE263573_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 PRJNA1098083 and SRA study SRP500569. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
14 conditions, mostly in duplicate
A.shNC ×2 A.shHDAC5 ×2 B.shNC ×2 B.shHDAC5 ×2 C.shNC ×2 C.shHDAC5 ×2 D.shNC ×2 D.shHDAC5 ×2 +10 more

Supports a between-group comparison across 28 samples.

How we read this: 14 replicated groups read from 32 sample titles; they account for 28 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 Pancreatic cancer datasets

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

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