GEO series

mTORC1-dependent suppression of autophagic activity in somatic cell nuclear transfer mouse embryos

GSE306587 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/09/01 Platform GPL34328Platform GPL21273

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: 5 conditions, mostly in triplicateGroups 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: mTORC1-dependent suppression of autophagic activity in somatic cell nuclear transfer mouse embryosReproduction (Cambridge, England) · 2025

Summary (written by the submitters)

Activation of autophagy after fertilization is essential for mammalian embryonic development, as it supplies embryos with nutrients and energy. Somatic cell nuclear transfer (SCNT) embryos frequently exhibit developmental arrest, largely because of incomplete genomic reprogramming; however, the role of non-genomic factors remains unclear.

Read the full summary ↓

Here, we investigated autophagy dynamics in mouse SCNT embryos using immunostaining and live-cell fluorescence imaging. In fertilized embryos, autophagy increased markedly from the late 2-cell stage and peaked at the morula stage. SCNT embryos followed a similar timeline but consistently showed reduced autophagic activity. Notably, the autophagic activity levels varied among SCNT embryos and positively correlated with their developmental potential. Attempts to enhance genomic reprogramming, including the removal of somatic histone methylation, did not restore autophagy. Instead, transcriptome analysis revealed ectopic activation of mTORC1 signaling as a likely cause of impaired autophagy. Consistently, treatment with an mTORC1 inhibitor successfully rescued the autophagic activity in SCNT embryos. These findings identify a persistent autophagy defect during preimplantation development in SCNT embryos and suggest that modulation of non-genomic pathways, such as mTORC1 signaling, could improve SCNT efficiency.

Published in

mTORC1-dependent suppression of autophagic activity in somatic cell nuclear transfer mouse embryos

Tatebe T, Pham DQ, Ogura A et al. · Reproduction (Cambridge, England) 2025 · PMID 41150827 · doi:10.1530/REP-25-0338

This dataset

Open GSE306587 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 GSE306587_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 PRJNA1311358 and SRA study SRP613448. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41150827) ↗

Study design

5 conditions, mostly in triplicate

IVF, 2-cell, ×3 IVF, 4-cell, ×3 SCNT, 2-cell, ×3 SCNT, 4-cell, ×3 Cumulus, ×2

Supports a between-group comparison across 14 samples.

How we read this: 5 replicated groups read from 14 sample titles; they account for 14 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

GSM9204269 IVF, 2-cell, rep1 IVF, 2-cell,
GSM9204270 IVF, 2-cell, rep2 IVF, 2-cell,
GSM9204271 IVF, 2-cell, rep3 IVF, 2-cell,
GSM9204272 IVF, 4-cell, rep1 IVF, 4-cell,
GSM9204273 IVF, 4-cell, rep2 IVF, 4-cell,
GSM9204274 IVF, 4-cell, rep3 IVF, 4-cell,
GSM9204275 SCNT, 2-cell, rep1 SCNT, 2-cell,
GSM9204276 SCNT, 2-cell, rep2 SCNT, 2-cell,
GSM9204277 SCNT, 2-cell, rep3 SCNT, 2-cell,
GSM9204278 SCNT, 4-cell, rep1 SCNT, 4-cell,
GSM9204279 SCNT, 4-cell, rep2 SCNT, 4-cell,
GSM9204280 SCNT, 4-cell, rep3 SCNT, 4-cell,
GSM9204281 Cumulus, rep1 Cumulus,
GSM9204282 Cumulus, rep2 Cumulus,

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