GEO series

Combinatorial miRNA activity is essential for transition of pluripotent cells into dormancy [dgcr8_RNA]

GSE244879 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/03/26 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 16 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: 16 samples: 4 × DGRC8 KO, not paused, vs 4 × DGRC8 KO, paused, vs 4 × WT, not paused, vs 4 × WT, paused,Groups 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.

Summary (written by the submitters)

Dormancy is a key feature of stem cell function in adult tissues as well as embryonic cells in the context of diapause. The establishment of dormancy is an active process that involves extensive transcriptional, epigenetic, and metabolic rewiring. How these processes are coordinated to successfully transition cells to the resting dormant state is not known.

Read the full summary ↓

Here we show that microRNA activity, which is normally dispensable for pre-implantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular, the pluripotent epiblast depends on miRNA activity, the absence of which results in loss of pluripotency and embryo collapse. Through small RNA profiling of individual embryos and computational integration of miRNA targets, we identified the miRNA-protein network of diapause. Individual miRNA function contributes to combinatorial regulation by the network and the perturbation of the network reduces embryo survival. Without miRNAs, nuclear and cytoplasmic bodies show aberrant expression. We identified the nutrient-sensitive transcription factor TFE3 as an upstream regulator of miRNA biogenesis, linking mTOR activity to miRNA induction. Our results reveal that miRNAs are critical for the transcriptional and structural rewiring of early embryos to establish dormancy.

This dataset

Open GSE244879 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 GSE244879_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 PRJNA1025267 and SRA study SRP465030. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

4 × DGRC8 KO, not paused, vs 4 × DGRC8 KO, paused, vs 4 × WT, not paused, vs 4 × WT, paused,

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

GSM7831302 DGRC8 KO, not paused, replicate 1 DGRC8 KO, not paused,
GSM7831303 DGRC8 KO, not paused, replicate 2 DGRC8 KO, not paused,
GSM7831304 DGRC8 KO, not paused, replicate 3 DGRC8 KO, not paused,
GSM7831305 DGRC8 KO, not paused, replicate 4 DGRC8 KO, not paused,
GSM7831306 DGRC8 KO, paused, replicate 1 DGRC8 KO, paused,
GSM7831307 DGRC8 KO, paused, replicate 2 DGRC8 KO, paused,
GSM7831308 DGRC8 KO, paused, replicate 3 DGRC8 KO, paused,
GSM7831309 DGRC8 KO, paused, replicate 4 DGRC8 KO, paused,
GSM7831310 WT, not paused, replicate 1 WT, not paused,
GSM7831311 WT, not paused, replicate 2 WT, not paused,
GSM7831312 WT, not paused, replicate 3 WT, not paused,
GSM7831313 WT, not paused, replicate 4 WT, not paused,
GSM7831314 WT, paused, replicate 1 WT, paused,
GSM7831315 WT, paused, replicate 2 WT, paused,
GSM7831316 WT, paused, replicate 3 WT, paused,
GSM7831317 WT, paused, replicate 4 WT, paused,

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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.