GEO series

Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [RNA-seq]

GSE221529 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/11/28 Platform GPL20301

At a glance

RNA-seq (gene expression) · human · 18 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 18 samples: 6 conditions, mostly in triplicateGroups 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: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degreeCell death & disease · 2023

Summary (written by the submitters)

The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. While mutations in the DNA binding domain of p53 cause cancer, mutations in the p63 DNA binding domain result in developmental syndromes affecting lip/palate, skin and limbs.

Read the full summary ↓

For p53 the effect of mutations has been studied in great detail, enabling the identification of several mechanisms by which mutations inhibit high affinity binding of p53 to DNA. In this study we provide a similar detailed investigation of all currently known mutations in the p63 DNA binding domain by measuring the transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes, to elicit changes in the transcriptional program similar to those observed by wild type p63, and to bind regulatory regions in the genome. The data demonstrate that no mutation globally destabilizes and unfolds the domain. Several mutations affect the DNA binding affinity by disturbing the interaction between the DNA binding domains, thereby disrupting p63 ability to bind DNA as a tetramer cooperatively. These mutations retain partial DNA binding capacity which correlates with a milder patient phenotype.

Published in

Osterburg C, Ferniani M, Antonini D et al. · Cell death & disease 2023 · PMID 37072394 · doi:10.1038/s41419-023-05796-y

This dataset

Open GSE221529 in finder → Find more human RNA-seq 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 GSE221529_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA914739 and SRA study SRP414334. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37072394) ↗

Study design

6 conditions, mostly in triplicate

RNAseq_BJ_WT_exp ×3 RNAseq_BJ_empty_exp ×3 RNAseq_BJ_R227Q_exp ×3 RNAseq_BJ_R298Q_exp ×3 RNAseq_BJ_R304W_exp ×3 RNAseq_BJ_R204W_exp ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM6883046 RNAseq_BJ_WT_exp1 RNAseq_BJ_WT_exp
GSM6883047 RNAseq_BJ_WT_exp2 RNAseq_BJ_WT_exp
GSM6883048 RNAseq_BJ_WT_exp3 RNAseq_BJ_WT_exp
GSM6883049 RNAseq_BJ_empty_exp1 RNAseq_BJ_empty_exp
GSM6883050 RNAseq_BJ_empty_exp2 RNAseq_BJ_empty_exp
GSM6883051 RNAseq_BJ_empty_exp3 RNAseq_BJ_empty_exp
GSM6883052 RNAseq_BJ_R227Q_exp1 RNAseq_BJ_R227Q_exp
GSM6883053 RNAseq_BJ_R227Q_exp2 RNAseq_BJ_R227Q_exp
GSM6883054 RNAseq_BJ_R227Q_exp3 RNAseq_BJ_R227Q_exp
GSM6883055 RNAseq_BJ_R298Q_exp1 RNAseq_BJ_R298Q_exp
GSM6883056 RNAseq_BJ_R298Q_exp2 RNAseq_BJ_R298Q_exp
GSM6883057 RNAseq_BJ_R298Q_exp3 RNAseq_BJ_R298Q_exp
GSM6883058 RNAseq_BJ_R304W_exp1 RNAseq_BJ_R304W_exp
GSM6883059 RNAseq_BJ_R304W_exp2 RNAseq_BJ_R304W_exp
GSM6883060 RNAseq_BJ_R304W_exp3 RNAseq_BJ_R304W_exp
GSM6883061 RNAseq_BJ_R204W_exp1 RNAseq_BJ_R204W_exp
GSM6883062 RNAseq_BJ_R204W_exp2 RNAseq_BJ_R204W_exp
GSM6883063 RNAseq_BJ_R204W_exp3 RNAseq_BJ_R204W_exp

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