GEO series

Nuclear Receptor-SINE B1 Network Modulates Expanded Pluripotency in Blastoids and Blastocysts [RNA-seq 1]

GSE293869 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2025/04/10 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 32 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: 32 samples: 16 conditions, mostly in duplicateGroups 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)

Embryonic stem cells possess the remarkable ability to self-organize into blastocyst-like structures upon induction. These synthetic embryo models serve as invaluable platforms for studying embryogenesis and therapeutic developments. Nevertheless, the specific intrinsic regulators that govern this potential for blastoid formation remain unknown.

Read the full summary ↓

Here we demonstrate a novel intrinsic program that plays a crucial role in both blastoids and blastocysts across multiple species. We first establish metrics for grading the resemblance of blastoids to mouse blastocysts, and identify the differential activation of gene regulons involved in lineage specification among various blastoid grades. Notably, abrogation of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) drastically reduces blastoid formation. Nr1h2 activation alone is sufficient to rewire conventional ESC into a distinct pluripotency state, enabling them to form blastoids with enhanced implantation capacity in the uterus and contribute to both embryonic and extraembryonic lineages in vivo. Through integrative multi-omics analyses, we uncover the broad regulatory role of Nr1h2 in the transcriptome, chromatin accessibility and epigenome, targeting genes associated with embryonic lineage and the transposable element SINE-B1. The Nr1h2-centred intrinsic program governs and drives the development of both blastoids and early embryos.

This dataset

Open GSE293869 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 GSE293869_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 PRJNA1246615 and SRA study SRP576600. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

16 conditions, mostly in duplicate

ESC, Passage 0, ×2 ESC, Passage 2, ×2 ESC, Passage 4, ×2 ESC, Passage 6, ×2 ESC, Passage 8, ×2 ESC, Passage 10, ×2 ESC, Passage 12, ×2 ESC, Passage 14, ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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

GSM8892239 ESC, Passage 0, Rep 1 ESC, Passage 0,
GSM8892240 ESC, Passage 0, Rep 2 ESC, Passage 0,
GSM8892241 ESC, Passage 2, Rep 1 ESC, Passage 2,
GSM8892242 ESC, Passage 2, Rep 2 ESC, Passage 2,
GSM8892243 ESC, Passage 4, Rep 1 ESC, Passage 4,
GSM8892244 ESC, Passage 4, Rep 2 ESC, Passage 4,
GSM8892245 ESC, Passage 6, Rep 1 ESC, Passage 6,
GSM8892246 ESC, Passage 6, Rep 2 ESC, Passage 6,
GSM8892247 ESC, Passage 8, Rep 1 ESC, Passage 8,
GSM8892248 ESC, Passage 8, Rep 2 ESC, Passage 8,
GSM8892249 ESC, Passage 10, Rep 1 ESC, Passage 10,
GSM8892250 ESC, Passage 10, Rep 2 ESC, Passage 10,
GSM8892251 ESC, Passage 12, Rep 1 ESC, Passage 12,
GSM8892252 ESC, Passage 12, Rep 2 ESC, Passage 12,
GSM8892253 ESC, Passage 14, Rep 1 ESC, Passage 14,
GSM8892254 ESC, Passage 14, Rep 2 ESC, Passage 14,
GSM8892255 NrESC, Passage 0, Rep 1 NrESC, Passage 0,
GSM8892256 NrESC, Passage 0, Rep 2 NrESC, Passage 0,
GSM8892257 NrESC, Passage 2, Rep 1 NrESC, Passage 2,
GSM8892258 NrESC, Passage 2, Rep 2 NrESC, Passage 2,
GSM8892259 NrESC, Passage 4, Rep 1 NrESC, Passage 4,
GSM8892260 NrESC, Passage 4, Rep 2 NrESC, Passage 4,
GSM8892261 NrESC, Passage 6, Rep 1 NrESC, Passage 6,
GSM8892262 NrESC, Passage 6, Rep 2 NrESC, Passage 6,
GSM8892263 NrESC, Passage 8, Rep 1 NrESC, Passage 8,
GSM8892264 NrESC, Passage 8, Rep 2 NrESC, Passage 8,
GSM8892265 NrESC, Passage 10, Rep 1 NrESC, Passage 10,
GSM8892266 NrESC, Passage 10, Rep 2 NrESC, Passage 10,
GSM8892267 NrESC, Passage 12, Rep 1 NrESC, Passage 12,
GSM8892268 NrESC, Passage 12, Rep 2 NrESC, Passage 12,
GSM8892269 NrESC, Passage 14, Rep 1 NrESC, Passage 14,
GSM8892270 NrESC, Passage 14, Rep 2 NrESC, Passage 14,

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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.