Background to this app
This app displays data described in Lynch et al. The EMBO Journal (link below): single cell RNA-seq (FLEX) data and analysis from hESC cardiac differentiation.
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, 4, 5, 6, 7, 8, and 10.
Plot info ('Gene expression', 'Cell types' and 'Trajectories' tabs)
- The 'Gene Expression' tab shows a UMAP plot coloured by the expression level of the selected gene. A threshold cutoff has been applied.
- The 'Cell types' tab shows a UMAP coloured by clusters / annotated cell type: MES = mesoderm, END = endoderm, MP = cardiac mesoderm progenitors, CP1 = early cardiac progenitors, CP2 = late cardiac progenitors, EPI = epicardial, FLC = fibroblast-like cells, EC = endothelial cells, CM = cardiomyocytes.
- The 'Trajectories' tab is coloured by pseudotime progression and displays the mesoderm differentiation lineages as identified by Monocle3. Two cardiac lineages are marked: FHF = first heart field, JCF = juxta-cardiac field, SHF = second heart field.
Data download info
The 'download' tab includes options to download the processed scRNA-seq data in different formats.
Reference
HAND1 level controls the specification of multipotent cardiac and extraembryonic progenitors from human pluripotent stem cells.
Lynch T, Phillips N, Douglas M, Dorgnach M, Lin H, Adamson AD, Darieva Z, Whittle J, Hanley NA, Bobola N, Birket MJ
The EMBO Journal, EMBO J (2025) 44: 2541 - 2565
https://doi.org/10.1038/s44318-025-00409-0Funders
Download options
Processed single cell RNA-seq data are available to download in Loom format via this link:
https://doi.org/10.48420/26935324Raw FASTQ data files are available via ArrayExpress E-MTAB-14285:
https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-14285Reference
HAND1 level controls the specification of multipotent cardiac and extraembryonic progenitors from human pluripotent stem cells.
Lynch T, Phillips N, Douglas M, Dorgnach M, Lin H, Adamson AD, Darieva Z, Whittle J, Hanley NA, Bobola N, Birket MJ
The EMBO Journal, EMBO J (2025) 44: 2541 - 2565
https://doi.org/10.1038/s44318-025-00409-0