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Identification of novel embryonic differentiation stage by combined cell tracking and high dimensional protein imaging

GSE259317 Mus musculus (mouse) Single-cell RNA-seq 57 samples Submitted 2024/08/19 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 57 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
57 samples: 19 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.
Paper
Identification of an embryonic differentiation stage marked by Sox1 and FoxA2 co-expression using combined cell tracking and high dimensional protein imagingNature communications · 2024
Summary (written by the submitters)
Pluripotent mouse embryonic stem cells (ESCs) can differentiate to all germ layers and serve as an in vitro model of embryonic development. To better understand the differentiation paths traversed by ESCs committing to different lineages, we tracked individual differentiating ESCs by timelapse imaging followed by multiplexed high-dimensional Imaging Mass Cytometry (IMC) protein quantification.
Read the full summary ↓
This links continuous live single-cell molecular NANOG and cellular dynamics quantification over 5-6 generations to protein expression of 37 different molecular regulators in the same single cells at the observation endpoints. Using this unique data set including kinship history and live lineage marker detection, we show that NANOG downregulation occurs generations prior to, but is not sufficient for neuroectoderm lineage commitment. Unexpectedly, we could identify a novel developmental cell type co-expressing both the canonical Sox1 neuroectoderm and FoxA2 endoderm markers in vitro and confirm the presence of such a population in the post-implantation embryo as well. RNASeq revealed cells co-expressing SOX1 and FOXA2 to have a unique cells state characterised by expression of both endoderm as well as neuroectoderm genes with lineage potential towards both germ layers.
Published in
Identification of an embryonic differentiation stage marked by Sox1 and FoxA2 co-expression using combined cell tracking and high dimensional protein imaging
Arekatla G, Skylaki S, Corredor Suarez D et al. · Nature communications 2024 · PMID 39251590 · doi:10.1038/s41467-024-52069-z
This dataset
Open GSE259317 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 GSE259317_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1080680 and SRA study SRP491845. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39251590) ↗
Study design
19 conditions, mostly in triplicate
Day0_Sox1-FoxA2 ×3 Day6_Sox1-FoxA2 ×3 Day6_Sox1+FoxA2 ×3 Day6_Sox1-FoxA2+ ×3 Day6_Sox1+FoxA2+ ×3 Day4_Sox1-FoxA2 ×3 Day4_Sox1+FoxA2 ×3 Day4_Sox1-FoxA2+ ×3 +11 more

Supports a between-group comparison across 57 samples.

How we read this: 19 replicated groups read from 57 sample titles; they account for 57 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

+ 17 more — browse all 57 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.