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Analysis of gene regulation by the TP63 isoforms deltaNp63alpha and deltaNp63beta using ChIPseq of p63 and H3K27ac

GSE283359 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 11 samples Submitted 2024/12/13 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 11 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)
Samples
11 samples: 5 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.
Paper
Differential Transcriptional Activity of ΔNp63β Is Encoded by an Isoform-Specific C-TerminusMolecular and cellular biology · 2025
Summary (written by the submitters)
Our goal was to assess transcriptional changes of the colon carcinoma cell line HCT116 TP53-/- in response to expression of the TP63 isoforms deltaNp63alpha or deltaNp63beta. The goal was to understand how these C-terminal isoforms of p63 might differentially regulate gene expression. We also assessed how differential binding of these isoforms and how they affect local changes in H3K27ac.
Published in
Differential Transcriptional Activity of ΔNp63β Is Encoded by an Isoform-Specific C-Terminus
McCann AA, Sammons MA · Molecular and cellular biology 2025 · PMID 40545896 · doi:10.1080/10985549.2025.2514529
This dataset
Open GSE283359 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE283359_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 PRJNA1193516 and SRA study SRP549001. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40545896) ↗
Study design
5 conditions, mostly in duplicate
HCT116 TP53-/-, deltaN ChIP, deltaNp63beta, ×2 HCT116 TP53-/-, deltaN ChIP, negControl, ×2 HCT116 TP53-/-, H3K27ac ChIP, deltaNp63alpha, ×2 HCT116 TP53-/-, H3K27ac ChIP, deltaNp63beta, ×2 HCT116 TP53-/-, H3K27ac ChIP, negControl, ×2 HCT116 TP53-/-, deltaN ChIP, deltaNp63alpha, ×1

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 11 sample titles; they account for 10 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
Datasets on a similar topic

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