GEO series

Maternal TDP43 Orchestrates Nuclear Speckle Assembly and Zygotic Splicing Activation During Oocyte-to-embryo Transition in Mouse [RNA-seq]

GSE278472 Mus musculus (mouse) RNA-seq (gene expression) 17 samples Submitted 2025/08/01 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 17 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: 17 samples
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: Maternal TDP43 orchestrates nuclear speckle assembly and zygotic splicing activation during oocyte-to-embryo transition in miceNucleic acids research · 2026

Summary (written by the submitters)

Zygotic splicing activation (ZSA) is an important means for mRNA post-transcriptional regulation during the maternal-to-zygotic transition (MZT) progress, ensuring normal embryonic development. However, the key factors and mechanisms of ZSA regulation are still unclear. Here, we found that nuclear speckle (NS), a key splicing region, is newly established at the 2-cell stage in mice, which is consistent with the period of ZSA.

Read the full summary ↓

Moreover, NS and TDP43, an important component of paraspeckle, always have a partially adjacent and mutually exclusive localization relationship. TDP43 shuttles from the paraspeckle through liquid-liquid phase separation to perform its function: that is, it acts as a match-maker, binding to the transcribed RNAs on the one hand, and directly binding to the NS proteins on the other hand to ensure the correct assembly of NS. Maternal TDP43 deficiency leads to NS assembly failure in 2-cells, resulting in the inability of transcripts to skip; while injection of excessive TDP43 in zygotes leads to abnormal enlargement of NS in 2-cells, resulting in excessive skipping of transcripts. Both bidirectional ZSA disorders lead to 2-cell arrest in early embryogenesis. The ZSA defect caused by TDP43 deficiency also impairs the cell totipotency-pluripotency conversion. Collectively, our study discovered a NS upstream regulatory factor TDP43, which help maintain the balance of ZSA, providing a new perspective on post-transcriptional regulation of early embryos.

Published in

Maternal TDP43 orchestrates nuclear speckle assembly and zygotic splicing activation during oocyte-to-embryo transition in mice

Deng ZQ, Jiang ZY, Wu YK et al. · Nucleic acids research 2026 · PMID 41521669 · doi:10.1093/nar/gkaf1469

This dataset

Open GSE278472 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 GSE278472_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 PRJNA1167327 and SRA study SRP535817. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41521669) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 17 more — browse all 17 samples with per-sample file links →

Datasets on a similar topic

GSE314859 The degradation of maternal RNA-binding protein 4E-T regulates translational activation to ensure maternal-to-zygotic transition in mouse embryos 67 samples shares activation, transition, maternal
GSE248222 Impact of Maternal Immune Activation and Sex on Placental and Fetal Brain Cytokine and Gene Expression Profiles in a Preclinical Model of Neurodevelopmental Disorders 64 samples shares activation, maternal
GSE99296 α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming 18 samples shares orchestrates, activation
GSE293592 Maternal immune activation delays DNA methylation and physiological maturation of cortical excitatory neurons 106 samples shares activation, maternal
GSE255212 Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interaction during Primordial Follicle Activation 762 samples shares activation
GSE331176 Phagosome-mediated activation of STING by purine and pyrimidine-based bacterial cyclic dinucleotides 380 samples shares activation
GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares activation
GSE297515 Piezo1-dependent activation of stromal cells ignites muscle inflammation in exercise and injury and is associated with inflammaging 90 samples shares activation

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.