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A rewiring of DNA replication mediated by MRE11 exonuclease underlies primed-to-naive cell de-differentiation

GSE254126 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/04/03 Platform GPL21626
At a glance

RNA-seq (gene expression) · mouse · 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
Mus musculus (mouse)
Samples
12 samples: 3 × D0_Primed vs 3 × D6_2i vs 3 × D6_2i_25uM vs 3 × D6_2i_50uMGroups 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
A rewiring of DNA replication mediated by MRE11 exonuclease underlies primed-to-naive cell de-differentiationCell reports · 2024
Summary (written by the submitters)
Mouse embryonic stem cells (mESCs) in the primed pluripotency state, that resembles the post-implantation epiblast, can be de-differentiated in culture to anaivestate that resembles the pre-implantation inner cell mass.We report that primed-to-naive mESC transition entails a significant slowdown of DNA replication forks and the compensatory activation of dormant origins.
Read the full summary ↓
Using iPOND (“isolation of proteins on nascent DNA”) coupled to mass spectrometry, we identify key changes in replisome composition that are responsible for these effects. Naive mESC forks are enriched in MRE11 nuclease and other DNA repair proteins. MRE11 is recruited to newly synthesized DNA in response to transcription-replication conflicts, and its inhibition or genetic downregulation in naive mESCs is sufficient to restore the fork speed observed in primed cells. Notably, MRE11 is required for the efficient primed-to-naive mESC transition, demonstrating a direct link between DNA replication dynamics and the mESC de-differentiation process
Published in
A rewiring of DNA replication mediated by MRE11 exonuclease underlies primed-to-naive cell de-differentiation
Ubieto-Capella P, Ximénez-Embún P, Giménez-Llorente D et al. · Cell reports 2024 · PMID 38581679 · doi:10.1016/j.celrep.2024.114024
This dataset
Open GSE254126 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 GSE254126_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 PRJNA1068604 and SRA study SRP485759. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38581679) ↗
Study design
3 × D0_Primed vs 3 × D6_2i vs 3 × D6_2i_25uM vs 3 × D6_2i_50uM

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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