scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular building blocks of the primary pacemaker

We present a high-resolution single-cell atlas of the whole developing heart in the zebrafish, a model organism increasingly used to study heart biology. Our data consisted of over 50 000 cells representing the building blocks of the zebrafish heart at 48 and 72 hpf, with two pseudoreplicates sequenced per time-point. We distinguished 18 discrete cell populations comprising major cardiac cell lineages and sublineages. Here, we provide our dataset as an accessible community resource envisaged to pave the way for in-depth analysis of cell populations with high specificity.
While we are in the process of publishing our work should you choose to use our data in your publication, please cite the preprint.

Abu Nahia K, Sulej A, Migdal M, Ochocka N, Ho R, Kaminska B, Zagorski M, Winata C,. scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular building blocks of the primary pacemaker. BioaRxiv:2023.06.26.546508. Available from: https://www.biorxiv.org/content/10.1101/2023.06.26.546508v1

Methods

Whole hearts were extracted from double transgenic individuals sqet31Et x Tg(myl7:mRFP) and sqet33mi59BEt x Tg(myl7:mRFP) and dissociated into single cells which were subsequently encapsulated according to the 10x Genomics workflow (detailed methods available in our publication). The transgenic lines sqet33mi59B and sqet31Et expressed EGFP in cells of the sinoatrial (SA) and atrioventricular (AV) pacemaker regions, which provided an internal control for rare cardiac cell populations. The transgenic line Tg(myl7:mRFP) was used to additionally demarcate cardiomyocytes (CMs), which is the most technically challenging cell type to isolate, and enhance cell clustering. Sequencing reads were mapped to the zebrafish reference genome GRCz11 (Ensembl release 100) extended with additional EGFP and mRFP sequences. Detailed parameters for cell filtering and downstream data processing can be found in our preprint.
Feel free to contact us for further enquiries: kanahia@iimcb.gov.pl, cwinata@iimcb.gov.pl and visit our lab webpage https://zdglab.iimcb.gov.pl/