← BioTransfer GEO Dataset Finder
GEO series

Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition

GSE236543 Mus musculus (mouse) RNA-seq (gene expression) 17 samples Submitted 2024/04/23 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 17 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
17 samples: 17 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
Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competitionDevelopmental cell · 2024
Summary (written by the submitters)
Organoids can undergo pattern formation by spontaneously forming spatially-localised signaling centers called organisers. Understanding how molecular pathways participate in this regulative process is a central challenge in biology. Here, we investigated self-organisation of a SHH-expressing floorplate in clonal neural tube organoids (NTOs).
Read the full summary ↓
In NTOs, a pulse of retinoic acid (RA) applied at Day 2 triggers self-organisation of a FOXA2+ floorplate by Day 6. FOXA2 expression was initially spatially scattered before resolving into multiple clusters. These FOXA2+ clusters underwent competition and physical sorting, resulting in a stable “winning” floorplate. We identified BMP signalling as a key governor of long-range cluster competition.
Published in
Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition
Krammer T, Stuart HT, Gromberg E et al. · Developmental cell 2024 · PMID 38776925 · doi:10.1016/j.devcel.2024.04.021
This dataset
Open GSE236543 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 GSE236543_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 PRJNA991548 and SRA study SRP447500. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38776925) ↗
Study design
17 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 17 sample titles: 17 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
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.