← BioTransfer GEO Dataset Finder
GEO series

DEPLETION OF TP53 IN HUMAN PLURIPOTENT STEM CELLS TRIGGERS MALIGNANT-LIKE BEHAVIOUR

GSE283179 Homo sapiens (human) RNA-seq (gene expression) 23 samples Submitted 2024/12/03 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 23 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
23 samples: 9 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
Depletion of TP53 in Human Pluripotent Stem Cells Triggers Malignant-Like BehaviorAdvanced biology · 2025
Summary (written by the submitters)
Human pluripotent stem cells (hPSCs) tend to acquire genetic aberrations upon culture in vitro. Common aberrations are mutations in the tumor suppressor TP53, suspected to confer a growth-advantage to the mutant cells. However, their full impact in the development of malignant features and safety of hPSCs for downstream applications is yet to be elucidated.
Read the full summary ↓
Here, we knock-out TP53 in hPSCs using CRISPR-Cas9 and compare them with isogenic wild-type hPSCs and human germ cell tumor lines as models of malignancy. While no major changes in proliferation, pluripotency and transcriptomic profiles are found, mutant lines display aberrations in some of the main chromosomal hotspots for genetic abnormalities in hPSCs. Additionally, enhanced clonogenic and anchorage-free growth, alongside resistance to chemotherapeutic compounds is observed. Our results indicate that common TP53-depleting mutations in hPSCs, although potentially overlooked by standard analyses, could impact their behavior and safety in a clinical setting.
Published in
Depletion of TP53 in Human Pluripotent Stem Cells Triggers Malignant-Like Behavior
Montilla-Rojo J, Eleveld TF, van Soest M et al. · Advanced biology 2025 · PMID 39760438 · doi:10.1002/adbi.202400538
This dataset
Open GSE283179 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 GSE283179_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 PRJNA1192284 and SRA study SRP548411. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39760438) ↗
Study design
9 conditions, mostly in duplicate
H9-p69plus ×3 HKO-p79plus ×3 2102Ep ×2 2102Ep-TP53-KO ×2 LKO3-p77plus ×2 LKO5-p71plus ×2 Lu07-p71plus ×2 NCCIT ×2 +4 more

Supports a between-group comparison across 20 samples.

How we read this: 9 replicated groups read from 23 sample titles; they account for 20 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

Search all human RNA-seq datasets in GEO →

Share this dataset

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.