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A DGCR8/FLII-dominated on-off switch for immediate-early genes governs embryo implantation in mouse and human [RNA-seq]

GSE256381 Mus musculus (mouse) RNA-seq (gene expression) 171 samples Submitted 2024/07/08 Platform GPL21273Platform GPL24247Platform GPL24676Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 171 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
171 samples: 47 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
A transient transcriptional activation governs unpolarized-to-polarized morphogenesis during embryo implantationMolecular cell · 2024
Summary (written by the submitters)
As an essential checkpoint for successful pregnancy, mammalian embryo implantation initiates fetal-maternal communication. However, the underlying transcriptional regulation governing such a fast transition is still unknown. Here, we identify a DGCR8/FLII-dominated on-off switch for immediate-early genes (IEGs) governing pluripotency transition and morphogenesis of epiblasts upon embryo implantation.
Read the full summary ↓
In mouse naïve embryonic stem cells (mESCs), we find the Microprocessor component DGCR8, but not DROSHA, can recognize mRNA stem-loop structures and further interact with and occupy transcriptional activator FLII to directly suppress transcription of non-miRNA target genes. Interestingly, when mESCs exit from naïve pluripotency, ERK signaling is quickly activated to induce FLII phosphorylation and disrupt DGCR8/FLII interaction. Phosphorylated FLII then binds to AP1, a typical IEG, to mediate the transcriptional activation of cell migration-related genes to establish poised pluripotency. Re-occupation of FLII by DGCR8 drives poised ESCs into formative pluripotency. Disruption of the DGCR8/FLII-mediated transcriptional activation inhibits the naïve-poised-formative ESC transition and the corresponding embryonic morphogenesis during implanting period, which is conserved in mouse and human.
Published in
A transient transcriptional activation governs unpolarized-to-polarized morphogenesis during embryo implantation
Lyu X, Cui Y, Kong Y et al. · Molecular cell 2024 · PMID 38955180 · doi:10.1016/j.molcel.2024.06.005
This dataset
Open GSE256381 in finder → Find more 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 GSE256381_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 PRJNA1079308 and SRA study SRP491079. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38955180) ↗
Study design
47 conditions, mostly in triplicate
WT mESC, ×3 Flii-/- mESC, ×3 DGCR8-/- mESC, ×3 DGCR8 FLII double knockouts mESC, ×3 Dicer-/- mESC, ×3 DGCR8 FLII double knockouts mESC, FLII rescue, ×3 DGCR8 FLII double knockouts mESC, FLII and D… ×3 DGCR8 FLII double knockouts mESC, FLII and DG… ×3 +69 more

Supports a case/control comparison: 12 samples read as cases, 37 as controls.

How we read this: 47 replicated groups read from 171 sample titles; they account for 141 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

+ 131 more — browse all 171 samples with per-sample file links →

Datasets on a similar topic

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