← BioTransfer GEO Dataset Finder
GEO series

Short term perturbation of mouse embryonic stem cells with morphogens and small molecule compounds

GSE202079 Mus musculus (mouse) RNA-seq (gene expression) 208 samples Submitted 2025/02/03 Platform GPL13112
At a glance

RNA-seq (gene expression) · mouse · 208 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
208 samples: 208 samples, each with a distinct title — no replicated groupsGroups 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
The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation developmentStem cell reports · 2024
Summary (written by the submitters)
Two strains of mouse embryonic stem cells were perturbed for 30h with 24 distinct small molecule compounds and for 24h with 5 differentiation morphogens.
Published in
The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development
Nakagawa S, Carnevali D, Tan X et al. · Stem cell reports 2024 · PMID 38701778 · doi:10.1016/j.stemcr.2024.04.004
This dataset
Open GSE202079 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 GSE202079_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 PRJNA834155 and SRA study SRP373248. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38701778) ↗
Study design
208 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 208 sample titles: 208 distinct titles with little repetition. 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

+ 168 more — browse all 208 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.