Integrative single-cell multi-modal analyses reveal detailed spatial cellular organization directing human heart morphogenesis

The heart, which is the first organ to develop, is highly dependent on its form to function. However, how diverse cardiac cell types spatially coordinate to create complex morphological structures critical for heart function remains to be elucidated. Here, we show that integration of single cell RNA-sequencing with high-resolution multiplexed error-robust fluorescent in situ hybridization (MERFISH) not only resolves the identity of cardiac cell types developing the human heart but also provides a spatial mapping of individual cells that enables illumination of their organization into cellular communities forming distinct cardiac structures. We discovered that many of these cardiac cell types further specified into subpopulations exclusive to specific communities, supporting their specialization according to cellular ecosystem and anatomic region. In particular, ventricular cardiomyocyte subpopulations displayed an unexpected complex laminar organization across the ventricular wall and ..., , , # Integrative single-cell multi-modal analyses reveal detailed spatial cellular organization directing human heart morphogenesis

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This data collection contains spatially resolved single-cell transcriptomics datasets acquired using MERFISH on the developing human heart (13 PCW heart and 15 PCW ventricles) collected by a collaboration of the Chi Lab and the Center for Epigenomics at the University of California, San Diego.

The heart sections were imaged with 238 genes using MERFISH with a 22-bit Hamming distance 4, Hamming weight 4, binary code. The 22 bits are imaged in 11 hybridization rounds with two-color imaging in each round. This human heart panel included 238 genes for MERFISH imaging and 20 genes for sequential, two-color FISH imaging following the MERFISH run.

## Description of the Data and file structure

* The dataset contains MERFISH images from a total of 4 experiments collected from two donors (3 x 13 PCW and 1 x 15 PCW). Each experiment was named with a sample_id ...