Background to this app

This app displays data described in Darieva et al. The EMBO Journal, In Press (link below): single cell RNA-seq (10X Chromium) and bulk RNA-seq from hESC cardiac differentiations.


Cell model info

Samples were from HES3 hESCs progressing through cardiac differentiation as 3D embryoid bodies. The scRNA-seq samples were collected at day 3, 3.75, 4.75, 5.75 and 12. The bulk RNA-seq data included a day 0 timepoint and each sample included biological replicates.


Plot info ('Data' tab)

  1. Plot 1 (top left), is a UMAP displaying clusters annotated by cell type: MES = mesoderm, END = endoderm, MP = cardiac mesoderm progenitors, CP1 = early cardiac progenitors, CP2 = late cardiac progenitors, EPI = epicardial, CM = cardiomyocytes.
  2. Plot 2 (bottom left), is a UMAP displaying the expression level of the selected gene.
  3. Plot 3 (top right), is a bar plot displaying the expression level of the selected gene by bulk RNA-seq (mean normalized counts) at 5 timepoints through differentiation.
  4. Plot 4 (bottom right), is a violin plot displaying the expression level of the selected gene in each cell type in the scRNA-seq data.

Data download info

The 'download' tab includes options to download the processed scRNA-seq data as a SingleCellExperiment object and the bulk RNA-seq data as a csv file.

Raw FASTQ data files will soon be available via ArrayExpress E-MTAB-14249 (scRNA-seq) and E-MTAB-14248 (bulk RNA-seq).


Reference

Ubiquitous MEIS transcription factors actuate lineage-specific transcription to establish cell fate

Darieva Z, Zarrineh P, Phillips N, Mallen J, Garcia Mora A, Donaldson I, Bridoux L, Douglas M, Dias Henriques SF, Schulte D, Birket MJ, Bobola N

The EMBO Journal, 2025

https://doi.org/10.1038/s44318-025-00385-5

Funders




Download options

Download single cell RNA-seq dataset (SingleCellExperiment.Rdata format)

Download1


Download bulk RNA-seq dataset (csv format)

Download2


Raw FASTQ data files for the scRNA-seq data will soon be available via ArrayExpress E-MTAB-14249:

https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-14249


Raw FASTQ data files for the bulk RNA-seq data will soon be available via ArrayExpress E-MTAB-14248:

https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-14248


Reference

The evolutionary ancient MEIS transcription factors actuate lineage-specific transcription to establish cardiac fate.

Darieva Z, Zarrineh P, Phillips N, Mallen J, Garcia Mora A, Donaldson I, Bridoux L, Douglas M, Dias Henriques SF, Schulte D, Birket MJ, Bobola N

bioRxiv 2024.07.18.604075

https://doi.org/10.1101/2024.07.18.604075