GEO series

Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts [RNA-seq]

GSE276877 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/10/23 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 14 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: Mus musculus (mouse)
Samples: 14 samples: 14 samples, each with a distinct title — no replicated groupsGroups 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: Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcriptsNature communications · 2025

Summary (written by the submitters)

Master transcription factors (MTFs) are key regulators in cell fate determination. However, an approach to profile MTF’s direct transcriptional targets together with their associated RNA-binding proteins (RBPs), is still lacking. Here, we applied 5-ethynyluridine RNA metabolic labelling and click chemistry to map the dynamics of the transcriptional targets and the RBPs interacting with the newly transcribed RNAs upon acute NANOG degradation in mouse embryonic stem cells (mESCs).

Read the full summary ↓

We identified UTP15, a classic rRNA-biogenesis regulator, acts as a key activator of pluripotency-associated gene transcription independently of rRNA biogenesis. Importantly, NANOG-regulated transcription enhances UTP15 binding to transcription start sites (TSSs), associated with increased Pol II binding and more active transcription. Moreover, UTP15 promotes the assembly of Pol II biomolecular condensates, thereby potentially driving pluripotency gene transcription. Collectively, our study uncovers a NANOG-nascent transcript-UTP15 regulatory axis to activate pluripotency gene transcription, providing a distinct approach for studying MTF’s function during cell fate determination.

Published in

Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts

Deng M, He D, Wang X et al. · Nature communications 2025 · PMID 41361183 · doi:10.1038/s41467-025-67018-7

This dataset

Open GSE276877 in finder → Find more mouse 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 GSE276877_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 PRJNA1159323 and SRA study SRP531898. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41361183) ↗

Study design

14 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 14 sample titles: 14 distinct titles with little repetition. 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

GSM8508096 NANOG_AID_0h-1_Total-RNA-seq
GSM8508097 NANOG_AID_0h-2_Total-RNA-seq
GSM8508098 NANOG_AID_2h-1_Total-RNA-seq
GSM8508099 NANOG_AID_2h-2_Total-RNA-seq
GSM8508100 NANOG_AID_4h-1_Total-RNA-seq
GSM8508101 NANOG_AID_4h-2_Total-RNA-seq
GSM8508102 NANOG_AID_48h-1_Total-RNA-seq
GSM8508103 NANOG_AID_48h-2_Total-RNA-seq
GSM8508104 UTP15_AID_0h-1_Total-RNA-seq
GSM8508105 UTP15_AID_0h-2_Total-RNA-seq
GSM8508106 UTP15_AID_24h-1_Total-RNA-seq
GSM8508107 UTP15_AID_24h-2_Total-RNA-seq
GSM8508108 UTP15_AID_48h-1_Total-RNA-seq
GSM8508109 UTP15_AID_48h-2_Total-RNA-seq

Datasets on a similar topic

GSE276878 Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts 16 samples shares nanog, utp15, pluripotency, degradation, transcripts, monitoring, regulating, maintains
GSE276879 Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts 30 samples shares nanog, utp15, pluripotency, degradation, transcripts, monitoring, regulating, maintains
GSE284224 Epitranscriptomic program promotes skeletal stem cell quiescence and pluripotency by regulating proteostasis via METTL3-FEM1B-GLI1 axis 44 samples shares pluripotency, regulating
GSE297660 WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity 18 samples shares nanog
GSE299636 WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [ChIP-seq] 28 samples shares nanog
GSE199855 shRNA-mediated silencing of candidate pluripotency regulators in mouse epibladst stem cells 798 samples shares pluripotency
GSE264615 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [RNA-seq] 123 samples shares pluripotency
GSE260522 Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development [RNA-seq] 86 samples shares degradation

Search all mouse RNA-seq datasets in GEO →

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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.