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Self-organised pattern formation in the developing dorsal neural tube by a temporal relay of BMP signalling

GSE247069 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2024/08/19 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 16 conditions, mostly in triplicateGroups 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)
Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study BMP signalling dynamicsin the vertebrateneural tube, we developed a new ES cell differentiation systemtailored for growing tissues.
Read the full summary ↓
Differentiating cellsform strikingself-organised pattern of dorsal neural tube cell typesdriven by sequential phases of BMP signalling that are observed both in vitro and in vivo.Data-driven biophysical modelling showed that thesedynamics result from coupling fast negative feedbackwithslow positive regulation of signalling bythe specification of an endogenousBMP source.Thus, in contrast to relays that propagate morphogen signalling in space, we uncover a BMP signallingrelay that operates intime. This mechanism allows rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation.Altogether, our study provides an experimental and theoretical framework to understand how signalling dynamicsis exploited indeveloping tissues.
This dataset
Open GSE247069 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 GSE247069_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 PRJNA1036160 and SRA study SRP470389. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
16 conditions, mostly in triplicate
mESC_RA_96h ×3 mESC_RAplus3ngB4_96h ×3 mESC_RA_144h ×3 mESC_RAplus5ngB4_80h ×3 mESC_RAplus1.5ngB4_96h ×3 mESC_RAplus3ngB4_80h ×3 mESC_RA_80h ×3 mESC_RAplus5ngB4_96h ×3 +8 more

Supports a between-group comparison across 48 samples.

How we read this: 16 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.