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Embryonic lumenogenesis is controlled by selective mRNA decay triggered by LIN28A relocation [iCLIP]

GSE169547 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2024/03/01 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 7 × lin28a-gfp-esc-naive vs 6 × lin28a-gfp-episc-primed vs 3 × lin28a-nls-gfp-esc-naive vs 3 × lin28a-esc-wtGroups 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
Poised PABP-RNA hubs implement signal-dependent mRNA decay in developmentNature structural & molecular biology · 2024
Summary (written by the submitters)
The naïve pluripotent epiblast cells become polarized into a rosette-like structure, followed by irreversible transition into primed pluripotency during one of the fastest morphological switches termed lumenogenesis. This requires rapid decay of pluripotency-associated mRNAs, but the underlying mechanism remains unknown. Guided by machine learning and metabolic RNA sequencing, we identified RNA binding proteins (RBPs), especially LIN28A, as primary mRNA decay factors.
Read the full summary ↓
To understand if RBP dynamics steer embryogenesis, we used mRNA-RBP interactome capture during naïve-rosette-epiblast-gastrulation progression. We identified a dramatic increase in LIN28A mRNA binding, driven by its nucleolus-to-cytoplasm translocation during the naïve-primed pluripotency transition. Cytoplasmic LIN28A binds to 3’UTRs of pluripotency-associated mRNAs to directly stimulate their decay, and thereby progression to lumenogenesis. Accordingly, forced nuclear retention of LIN28A impeded lumenogenesis, causing an unforeseen embryonic multiplication and impaired gastrulation. This reveals selective mRNA decay, driven by nucleo-cytoplasmic RBP translocation, as an intrinsic mechanism for cell identity switch that controls embryonic timing of lumenogenesis.
Published in
Poised PABP-RNA hubs implement signal-dependent mRNA decay in development
Modic M, Kuret K, Steinhauser S et al. · Nature structural & molecular biology 2024 · PMID 39054355 · doi:10.1038/s41594-024-01363-x
This dataset
Open GSE169547 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 GSE169547_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 PRJNA716992 and SRA study SRP311988. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39054355) ↗
Study design
7 × lin28a-gfp-esc-naive vs 6 × lin28a-gfp-episc-primed vs 3 × lin28a-nls-gfp-esc-naive vs 3 × lin28a-esc-wt

Supports a between-group comparison across 19 samples.

How we read this: 4 replicated groups read from 20 sample titles; they account for 19 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
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