GEO series

Lineage-specific enhancer insertions regulate Prdm14 to drive the rapid transition from naïve to formative pluripotency in rodents

GSE309484 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/11/20 Platform GPL21273

At a glance

RNA-seq (gene expression) · mouse · 16 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: 16 samples: 8 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: Lineage-specific enhancer insertions regulate Prdm14 to drive the rapid transition from naïve to formative pluripotency in rodentsDevelopment (Cambridge, England) · 2025

Summary (written by the submitters)

The network of transcription factors is dynamically reorganized during the transition from naïve to formative pluripotency. In mice, Prdm14 is expressed in naïve pluripotent cells but rapidly downregulated upon exit from the naïve state. In contrast, PRDM14 expression persists throughout pluripotency transitions in non-rodent mammals, including pigs and humans.

Read the full summary ↓

Here, we investigate the molecular mechanisms underlying the rodent-specific expression of Prdm14. Using CRISPR/Cas9-mediated deletions, we demonstrated that OCT4 and TFCP2L1 recognition sequences within Muroidea-specific cis-regulatory elements located downstream of Prdm14 are essential for its transcriptional upregulation required for the upregulation of Prdm14 in naive embryonic stem cells (ESCs). Loss of these enhancers suppresses Pramel7 induction and impairs degradation of UHRF1, thereby attenuating global DNA demethylation under 2iL conditions. Moreover, deletion of PRDM14-binding motifs in Muroidea-specific enhancers disrupts its negative feedback loop, resulting in delayed transition from the naïve to formative pluripotent state.

Published in

Lineage-specific enhancer insertions regulate Prdm14 to drive the rapid transition from naïve to formative pluripotency in rodents

Matsubara K, Hirota M, Kajiwara K et al. · Development (Cambridge, England) 2025 · PMID 41267649 · doi:10.1242/dev.204886

This dataset

Open GSE309484 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 GSE309484_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 PRJNA1336162 and SRA study SRP629566. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41267649) ↗

Study design

8 conditions, mostly in duplicate

E14tg2a, WT_2i ×2 E14tg2a, WT_d2 ×2 E14tg2a, WT_d4 ×2 E14tg2a, DKO_2i ×2 E14tg2a, DKO_d2 ×2 E14tg2a, DKO_d4 ×2 E14tg2a, P14_d2 ×2 E14tg2a, P14_d4 ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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

GSM9268014 E14tg2a, WT_2i_rep1 E14tg2a, WT_2i
GSM9268015 E14tg2a, WT_2i_rep2 E14tg2a, WT_2i
GSM9268016 E14tg2a, WT_d2_rep1 E14tg2a, WT_d2
GSM9268017 E14tg2a, WT_d2_rep2 E14tg2a, WT_d2
GSM9268018 E14tg2a, WT_d4_rep1 E14tg2a, WT_d4
GSM9268019 E14tg2a, WT_d4_rep2 E14tg2a, WT_d4
GSM9268020 E14tg2a, DKO_2i_rep1 E14tg2a, DKO_2i
GSM9268021 E14tg2a, DKO_2i_rep2 E14tg2a, DKO_2i
GSM9268022 E14tg2a, DKO_d2_rep1 E14tg2a, DKO_d2
GSM9268023 E14tg2a, DKO_d2_rep2 E14tg2a, DKO_d2
GSM9268024 E14tg2a, DKO_d4_rep1 E14tg2a, DKO_d4
GSM9268025 E14tg2a, DKO_d4_rep2 E14tg2a, DKO_d4
GSM9268026 E14tg2a, P14_d2_rep1 E14tg2a, P14_d2
GSM9268027 E14tg2a, P14_d2_rep2 E14tg2a, P14_d2
GSM9268028 E14tg2a, P14_d4_rep1 E14tg2a, P14_d4
GSM9268029 E14tg2a, P14_d4_rep2 E14tg2a, P14_d4

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