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TBP regulates transposable element expression in early mouse embryos [RNA-seq]

GSE288110 Mus musculus (mouse) RNA-seq (gene expression) 49 samples Submitted 2025/12/15 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 49 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
49 samples: 6 conditions, mostly with about 10 replicates eachGroups 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
TBP regulates transposable element expression in early mouse embryosThe EMBO journal · 2026
Summary (written by the submitters)
Activation of the embryonic genome is a crucial step in development. In addition to thousands of genes, many transposable elements (TEs) are robustly transcribed during early mammalian development. However, their transcriptional regulators remain largely unexplored. Here, we set out to identify transcription factors regulating the expression of highly expressed TEs from the LINE, SINE and ERVL families during mouse preimplantation development.
Read the full summary ↓
In particular, the MaLR family are the most abundant ERVL in the mouse genome and are also the most abundant constituent of the transcriptome in early mouse embryos. Surprisingly, we find the general transcription factor TBP directly and specifically activates MaLRs. Loss-of-function of TBP in mouse embryos leads to downregulation of MaLRs, specifically the ORR1A family, which is the youngest ORR subclass and contributes a significant portion of major zygotic genome activation transcripts. We demonstrate that TBP regulates MaLRs through direct binding. Our work contributes to the identification of regulators of TE expression in vivo and highlights a previously unrecognised role for a general transcription factor in regulating an exquisitely specific TE transcriptional programme.
Published in
TBP regulates transposable element expression in early mouse embryos
Hermant C, Mourra-Díaz CM, Oomen ME et al. · The EMBO journal 2026 · PMID 41862641 · doi:10.1038/s44318-026-00736-w
This dataset
Open GSE288110 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 GSE288110_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 PRJNA1216206 and SRA study SRP560154. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41862641) ↗
Study design
6 conditions, mostly with about 10 replicates each
mIGG_CONTROL_Embryo ×10 FOXJ3_LOF_Batch1_Embryo ×10 Tbp_LOF_Embryo ×9 rIGG_CONTROL_Batch1_Embryo ×7 FOXJ3_LOF_Batch2_Embryo ×7 rIGG_CONTROL_Batch2_Embryo ×6

Supports a between-group comparison across 49 samples.

How we read this: 6 replicated groups read from 49 sample titles; they account for 49 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

+ 9 more — browse all 49 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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