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Analysis of gene regulation by the TP63 isoforms deltaNp63alpha and deltaNp63beta

GSE283357 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/12/13 Platform GPL11154
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × deltaNp63alpha,HCT116,TP53-/-,water, vs 3 × deltaNp63alpha,HCT116,TP53-/-,500ng/mL doxycycline, vs 3 × deltaNp63beta,HCT116,TP53-/-,water, vs 3 × deltaNp63beta,HCT116,TP53-/-,500ng/mL doxycycline,Groups 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)
We analyzed the transcriptome 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.
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 GSE283357 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 GSE283357_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 PRJNA1193517 and SRA study SRP548999. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40545896) ↗
Study design
3 × deltaNp63alpha,HCT116,TP53-/-,water, vs 3 × deltaNp63alpha,HCT116,TP53-/-,500ng/mL doxycycline, vs 3 × deltaNp63beta,HCT116,TP53-/-,water, vs 3 × deltaNp63beta,HCT116,TP53-/-,500ng/mL doxycycline,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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