Dataset DOI: 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