GEO series

Tumor suppresson protein p53 governs human trophoblast lineage development

GSE277265 Homo sapiens (human) Single-cell RNA-seq 32 samples Submitted 2025/09/22 Platform GPL24676Platform GPL24247

At a glance

Single-cell RNA-seq · human · 32 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 32 samples: 16 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: Tumor suppressor protein p53 governs human trophoblast lineage developmentCell reports · 2025

Summary (written by the submitters)

In addition to being a potent tumor suppressor, the p53 protein (encoded by Trp53 in mouse and TP53 in human) has important functions in embryo development and stem cells. The Trp53-null mice exhibit developmental defects whereas p53 activation causes implantation failure. However, it remains unclear how p53 affects early embryonic cell lineage development.

Read the full summary ↓

We report here that p53 is highly expressed in the trophectoderm (TE) of the blastocyst and that blocking p53 activities arrests preimplantation embryo development. We have subsequently investigated p53 using human pluripotent stem cells (hPSCs) in the generation of human trophoblast stem cells (hTSCs). Genetic ablation of TP53 or chemical inhibition of p53 activities hinders the generation of hTSCs while enhancing the generation of amniotic cells. Furthermore, p53 deficiency in hTSCs results in epigenetic dysregulation of the trophoblast regulatory network involving the generation of mature syncytiotrophoblasts (STBs). In contrast, the generation and invasiveness of extravillous trophoblasts (EVTs) is enhanced. Single-cell transcriptomics analysis and experimental investigation further revealed the importance of p53 functions at multiple stages of human trophoblast development and identify that p53-mediated cell-cycle state determines trophoblast cell fate propensity. These findings for the first time demonstrate the important functions of p53 in human early embryonic cell lineage development and implicate possible links between the role of p53 in early development and tumor suppression.

Published in

Tumor suppressor protein p53 governs human trophoblast lineage development

Huang Y, Xu L, Fu H et al. · Cell reports 2025 · PMID 40971294 · doi:10.1016/j.celrep.2025.116310

This dataset

Open GSE277265 in finder → Find more 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 GSE277265_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1161618 and SRA study SRP532911. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40971294) ↗

Study design

16 conditions, mostly in duplicate

Mouse embryos, 20h DMSO, ×2 Mouse embryos, 20h p53 inhibition, ×2 EPSC, WT, ×2 EPSC, TP53KO, ×2 Differentiated, D2 WT, ×2 Differentiated, D2 TP53KO, ×2 Differentiated, D4 WT, ×2 Differentiated, D4 TP53KO, ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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

GSM8517346 Mouse embryos, 20h DMSO, rep1 Mouse embryos, 20h DMSO,
GSM8517347 Mouse embryos, 20h DMSO, rep2 Mouse embryos, 20h DMSO,
GSM8517348 Mouse embryos, 20h p53 inhibition, rep1 Mouse embryos, 20h p53 …
GSM8517349 Mouse embryos, 20h p53 inhibition, rep2 Mouse embryos, 20h p53 …
GSM8517350 EPSC, WT, rep1 EPSC, WT,
GSM8517351 EPSC, WT, rep2 EPSC, WT,
GSM8517352 EPSC, TP53KO, rep1 EPSC, TP53KO,
GSM8517353 EPSC, TP53KO, rep2 EPSC, TP53KO,
GSM8517354 Differentiated, D2 WT, rep1 Differentiated, D2 WT,
GSM8517355 Differentiated, D2 WT, rep2 Differentiated, D2 WT,
GSM8517356 Differentiated, D2 TP53KO, rep1 Differentiated, D2 TP53…
GSM8517357 Differentiated, D2 TP53KO, rep2 Differentiated, D2 TP53…
GSM8517358 Differentiated, D4 WT, rep1 Differentiated, D4 WT,
GSM8517359 Differentiated, D4 WT, rep2 Differentiated, D4 WT,
GSM8517360 Differentiated, D4 TP53KO, rep1 Differentiated, D4 TP53…
GSM8517361 Differentiated, D4 TP53KO, rep2 Differentiated, D4 TP53…
GSM8517362 Differentiated, D7 WT, rep1 Differentiated, D7 WT,
GSM8517363 Differentiated, D7 WT, rep2 Differentiated, D7 WT,
GSM8517364 Differentiated, D7 TP53KO, rep1 Differentiated, D7 TP53…
GSM8517365 Differentiated, D7 TP53KO, rep2 Differentiated, D7 TP53…
GSM8517366 TSC, WT, rep1 TSC, WT,
GSM8517367 TSC, WT, rep2 TSC, WT,
GSM8517368 TSC, TP53KO, rep1 TSC, TP53KO,
GSM8517369 TSC, TP53KO, rep2 TSC, TP53KO,
GSM9071128 EVT, WT, D3, rep1 EVT, WT, D3,
GSM9071129 EVT, WT, D3, rep2 EVT, WT, D3,
GSM9071130 EVT, TP53KO, D3, rep1 EVT, TP53KO, D3,
GSM9071131 EVT, TP53KO, D3, rep2 EVT, TP53KO, D3,
GSM9071132 EVT, WT, D6, rep1 EVT, WT, D6,
GSM9071133 EVT, WT, D6, rep2 EVT, WT, D6,
GSM9071134 EVT, TP53KO, D6, rep1 EVT, TP53KO, D6,
GSM9071135 EVT, TP53KO, D6, rep2 EVT, TP53KO, D6,

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