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Deciphering lineage specification during early embryogenesis using integrative multi-layered proteomics [RNA-Seq]

GSE252488 Homo sapiens (human) Single-cell RNA-seq 24 samples Submitted 2024/05/21 Platform GPL30173Platform GPL30172
At a glance

Single-cell RNA-seq · human · 24 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
Homo sapiens (human)
Samples
24 samples: 8 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
Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomicsCell stem cell · 2024
Summary (written by the submitters)
Gastrulation is a critical stage in embryonic development during which the germ layers are established. The advances and increasing availability of sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and its derivatives. However, proteome-based studies of early mammalian development are scarce.
Read the full summary ↓
To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho)protein expression during gastruloid differentiation. Our findings revealed that many proteins exhibit temporal expression with unique expression profiles corresponding to the three germ layers, which we also validated using single-cell proteomics technology. Notably, detected temporal protein expression dynamics in gastruloids aligns with equivalent mouse embryo stages. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with scRNA-seq identified a critical role for ZEB2 in regulating mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
Published in
Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics
Stelloo S, Alejo-Vinogradova MT, van Gelder CAGH et al. · Cell stem cell 2024 · PMID 38754429 · doi:10.1016/j.stem.2024.04.017
This dataset
Open GSE252488 in finder → Find more 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 GSE252488_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 PRJNA1060726 and SRA study SRP481170. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38754429) ↗
Study design
8 conditions, mostly in triplicate
RNAseq_mouse_gastruloids_0h ×3 RNAseq_mouse_gastruloids_48h ×3 RNAseq_mouse_gastruloids_72h ×3 RNAseq_mouse_gastruloids_96h ×3 RNAseq_mouse_gastruloids_120h ×3 RNAseq_human_somitoids_WT ×3 RNAseq_human_somitoids_ZEB2_HetKO ×3 RNAseq_human_somitoids_ZEB2_HomKO ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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