DOI: 10.5061/dryad.j0zpc86v9
title: Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis

description: This dataset supports a whole-embryo investigation of the spatial and
 temporal regulation of gene expression during early zebrafish development.
 It includes high-resolution weMERFISH measurements of 495 genes at
 subcellular resolution across three developmental stages (50%
 epiboly/early gastrula, 75% epiboly/mid gastrula, and 6-somite stage/early
 organogenesis), together with imputed spatial expression patterns for
 25,872 additional genes. For each embryo, the dataset provides cell-level
 transcript counts, spatial coordinates, subcellular localization of
 individual transcripts, and corresponding tissue and cluster annotations.
 In addition, the dataset contains the MERFISH-FATE cell correspondence
 tables that link fixed embryos to whole-embryo live imaging, enabling
 analysis of gene expression changes in the context of cell movements and
 lineage trajectories. These data collectively form a comprehensive spatial
 multiomics atlas of zebrafish gastrulation and early organogenesis,
 supporting studies of gene regulation, tissue patterning, boundary
 formation, and the integration of molecular and morphogenetic processes.
description: # Whole-embryo spatial transcriptomics at subcellular resolution from
 gastrulation to organogenesis Dataset DOI:
 [10.5061/dryad.j0zpc86v9](https://doi.org/10.5061/dryad.j0zpc86v9) ##
 Description of the data and file structure weMERFISH data, containing
 single-cell measured and imputed gene expression, and subcellular
 localization data of individual transcripts. This dataset includes
 whole-embryo spatial transcriptomics measurements for 495 genes acquired
 at subcellular resolution across three zebrafish developmental stages,
 together with imputed spatial expression patterns for 25,872 additional
 genes generated through integration with single-cell multiome data. For
 each embryo, the dataset provides cell-level transcript counts, 3D spatial
 coordinates, transcript-level subcellular positions, and tissue and
 cluster annotations. The repository also contains the MERFISH-FATE
 correspondence tables that link fixed embryos to whole-embryo live
 imaging, enabling exploration of gene expression dynamics in the context
 of cell movement and lineage trajectories. ### Files and variables **The
 following files contain location of the single RNA molecules** *
 RNA_loc_A_50p_E1.csv * RNA_loc_A_50p_E2.csv * RNA_loc_B_75p_E1.csv *
 RNA_loc_B_75p_E2.csv * RNA_loc_C_6s_E1.csv * RNA_loc_C_6s_E2.csv Column
 data correspond to  * : transcript ID * z,x,y: coordinates of the
 transcripts in imaging/pixel space * Cor_: signal correlation with
 Gaussian * Xdist_: distance between the three decoded dots * Hraw: raw
 intensity * memdist: distance to membrane in 3D * memdist2d: distance to
 membrane in 2D * isnuc: whether the transcript is in nuclei (TRUE) or
 cytoplasm (FALSE) * icodesN: MERFISH codebook ID * cid: cell ID * gene:
 gene name **The following files contain measured weMERFISH signal assigned
 to single cells** * weMERFISH_measured_A_50p_E1.h5ad *
 weMERFISH_measured_A_50p_E2.h5ad * weMERFISH_measured_B_75p_E1.h5ad *
 weMERFISH_measured_B_75p_E2.h5ad *
 weMERFISH_measured_C_6s_E1_rescaled_z.h5ad *
 weMERFISH_measured_C_6s_E2_rescaled_z.h5ad Two datasets/embryos (E1 and
 E2) per developmental stage, with single-cell measurements in the format
 of scanpy AnnData: adata.obsm[‘X_raw’] contains the measured gene levels
 (dimensions same as adata.X) adata.obs[‘clusters’] contains cluster
 annotation of the cells. For 50% epiboly (A_50p) and 75% epiboly (B_75p)
 data, adata.obsm[‘global_sphere’] has the spherical coordinates (x,y,z)
 adata.obs[‘theta’] and adata.obs[‘phi’] contains the polar coordinates of
 the cells on the sphere. For 6-somite stage (C_6s) data
 adata.obsm[‘spatial’] should be used to visualize the coordinates, with z
 scaled to real-world sample thickness **The following files contain
 imputed gene expression data from scMultiome data:** *
 weMERFISH_combined_A_50p_E1.h5ad * weMERFISH_combined_A_50p_E2.h5ad *
 weMERFISH_combined_B_75p_E1.h5ad * weMERFISH_combined_B_75p_E2.h5ad *
 weMERFISH_combined_C_6s_E1_rescaled_z.h5ad *
 weMERFISH_combined_C_6s_E2_rescaled_z.h5ad It contains the data structure
 above as weMERFISH_measured, and additionally: adata.obsm[‘X_imputed’]
 contains the imputed gene levels adata.uns[‘imputed_gene_names’] contains
 the name of the imputed genes in the matrix above **For MERFISH-FATE** The
 two pairs of datasets [matched_A_50p_E1_sphere_logFC.h5ad and
 matched_B_75p_E1_sphere_logFC.h5ad] and
 [matched_A_50p_E2_sphere_logFC.h5ad and
 matched_B_75p_E2_sphere_logFC.h5ad] are weMERFISH datasets connected by
 live imaging data. Cells with the same .obs['weMERFISH_id']
 indicate the corresponding lineage/spatial locations. The matched cell ID
 in live tracking dataset is stored in .obs['Amat_id'], which
 corresponds to the first column of the csv file listed below.
 Tracking_Matrix.csv is the tracking result of the live imaging data, with
 TM0 being 50% epiboly and TM230 being 75% epiboly.  Variables * node id:
 ID of the cell * timepoint: time point of the cell in the movie, time step
 is 90s * x: x coordinates  * y: y coordinates  * z: z coordinates  *
 number of children: number of children of the listed cell * number of
 parents: number of paretns of the listed cell * sum number of children and
 parents: number of children and parents of the listed cell * child 1 id:
 child 1 cell ID, correspond the the first column * child 2 id: child 2
 cell ID, correspond the the first column * parent id: parent cell ID,
 correspond the the first column * ancestor id: ancestor cell ID from time
 point 0 or when the lineage started ## Code/software Python 3.9.13 scanpy
 1.10.3