DOI: 10.5061/dryad.w0vt4b8vp
title: Integrative single-cell multi-modal analyses reveal detailed spatial cellular organization directing human heart morphogenesis

description: 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 formed, with other cell subpopulations, several
 cellular communities. Interrogating cell-cell interactions within these
 communities revealed signaling pathways orchestrating the spatial
 organization of cardiac cell subpopulations during ventricular wall
 morphogenesis. In vivo conditional genetic mouse models and in
 vitro human pluripotent stem cell studies confirmed an intricate
 multicellular PLXN-SEMA crosstalk among specific ventricular
 cardiomyocyte, fibroblast and endothelial cell subpopulations that directs
 the compaction of the ventricular wall layers. Thus, these detailed
 findings into the cellular social interactions and specialization of
 cardiac cell types constructing and remodeling the human heart offer new
 insights into structural heart diseases as well as engineering complex
 multi-cellular tissues for human heart repair.
description: # Integrative single-cell multi-modal analyses reveal detailed spatial
 cellular organization directing human heart morphogenesis --- 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 that is
 composed of the imaging experiment id and replicate id. For instance, in
 'R1_R77_4C4', R1 is replicate 1, and R77_4C4 is the imaging
 experiment id. R77_4C4, R78_4C12, and R78_4C15 correspond to the 13 PCW
 heart, while R123_N3S5 corresponds to the 15 PCW ventricles. This folder
 contains the following files: 1.
 {Replicate}_{sample_id}*assigned_barcodes.csv: Decoded RNA spot location
 (global_x,global_y) in the unit of microns and their gene identity for
 each experiment and the cell id that each molecule belongs to for each
 experiment. 2. {Replicate}*{sample_id}*single_cell_raw_counts.csv.
 Cell-by-gene matrix for each experiment. 3.
 {Replicate}*{sample_id}_cell_metadata.csv: Metadata information of each
 sample. Contains volume (size of cell) information for each cell_id, as
 well as fov, global_x, global_y, and status from the 'assignedFor
 each cell id, it contains the field 4. overall_merfish.h5ad: Scanpy object
 of the three replicate MERFISH experiments of a 13 PCW heart 5.
 ventricle_merfish.h5ad: Scanpy object of a ventricle subset of the 13 PCW
 MERFISH experiments 6. ventricle_15pcw_merfish.h5ad: Scanpy object of a
 MERFISH experiment of 15 PCW ventricles 7. overall_heart.rds: Seurat
 object of scRNA-seq from 9 PCW, 11 PCW, 13 PCW, and 15 PCW hearts 8.
 cardiomyocyte_compartment.rds: Seurat object of a cardiomyocyte subset of
 the overall_heart.rds object 9. mesenchymal_compartment.rds: Seurat object
 of a mesenchymal subset of the overall_heart.rds object 10.
 endothelial_compartment.rds: Seurat object of a endothelial subset of the
 overall_heart.rds object 11. neuronal_compartment.rds: Seurat object of a
 neuronal subset of the overall_heart.rds object 12. blood_compartment.rds:
 Seurat object of a blood subset of the overall_heart.rds object Columns in
 the **assigned_barcodes.csv** table: Barcode_id The codebook index of the
 barcode, i.e. the gene. The gene column is more useful. Fov Which field of
 view (fov) the barcode is in X,Y,Z The pixel coordinates of the barcode
 within the FOV image. X and y range from 0 to 2048, with each pixel being
 ~108nm (the FOV is 220 microns). The Z coordinate is from 0 to 19, with
 each unit being 600nm. Gene The name of the gene for this barcode
 Error_type, Error_bit Error_type=0 means no error was corrected, -1 is a
 1-&gt;0 error corrected, +1 is a 0-&gt;1 error corrected. Error_bit is the
 bit the error occurred in. Status The status of the barcode. If you want
 all barcodes ignoring cell segmentation, filter out barcodes with status
 “edge” and keep all the rest. If you want the barcodes kept after applying
 the cell segmentation and filtering, only use the barcodes with status
 “good”. Cell_id The cell ID this barcode was assigned to, or 0 if no cell.
 global_x, global_y Barcode position converted to global coordinates, in
 micron units. Columns in the **cell_metadata.csv** table: Cell_id The
 assigned ID for each identified cell. Fov Which field of view (fov) the
 cell is in Volume The calculated size of the cell. global_x, global_y Cell
 position converted to global coordinates, in micron units. Status The
 status of the cell. Cells are filtered on volume and whether it contained
 detected barcodes. If you want the cells kept after applying filtering,
 only use the cells with status “ok”. Details for h5ad files:
 overall_merfish.h5ad - AnnData object containing the following information
 for each cell: 'sample_id' (experimental ID), 'batch'
 (experimental ID, same as sample_id for this object), 'n_counts'
 (number of transcript counts), 'leiden' (assigned cluster
 number), 'zone_cluster' (assigned cellular community number),
 'communities' (assigned cellular community name),
 'complexity' (number of unique populations in 150 micron cell
 zone), 'populations' (assigned population name),
 'purity' (proportion of majority cell population within 150
 micron cell zone) ventricle_merfish.h5ad - AnnData object containing the
 following information for each cell: 'sample_id' (experimental
 ID), 'batch' (experimental ID, same as sample_id for this
 object), 'n_counts' (number of transcript counts),
 'leiden' (assigned cluster number), 'zone_cluster'
 (assigned cellular community number), 'communities' (assigned
 cellular community name), 'complexity' (number of unique
 subpopulations in 150 micron cell zone), 'populations' (assigned
 population name), 'purity' (proportion of majority cell
 subpopulation within 150 micron cell zone), 'subpopulations'
 (assigned ventricular subpopulation name), 'depth' (depth within
 ventricular wall) ventricle_15pcw_merfish.h5ad - AnnData object containing
 the following information for each cell: 'n_genes' (number of
 genes), 'n_genes_by_counts' (number of genes),
 'log1p_n_genes_by_counts' (number of genes log transformed),
 'total_counts' (number of transcript counts),
 'log1p_total_counts' (number of transcript counts log
 transformed), 'subpopulations' (assigned ventricular
 subpopulation name) ## Sharing/access Information Links to other publicly
 accessible locations of the data: 
 Was data derived from another source? No