This CZ CELLxGENE session enables visualization of splicing differences in the Tabula Sapiens atlas. For each cell, a splicing score, called the SpliZ, is assigned to each gene with enough informative splicing information (Olivieri et. al. 2022). This object contains both gene expression values (labeled with the gene name, e.g. “MYL6”) and splicing values (labeled with the gene name and “SpliZ”, e.g. “MYL6_SpliZ”). Low SpliZ values correspond to shorter introns on average across the gene, while high SpliZ values correspond to longer introns on average. The splice junctions for each gene in a cell have been called based on the SICILIAN method (Dehghannasiri et. al., 2021).
The following metadata categories are available:
- donor: Set of donors available in the dataset. For details see the donor characteristics summary
- organ_tissue: List of organs available in Tabula Sapiens.
- anatomical_information: If available, more specific information of where in the organ the cells were collected is provided.
- gender: Gender of donors available in the dataset. For details see the donor characteristics summary.
- cell_ontology_class: Cell type annotations using the Cell Ontology.
- free_annotation: Cell type annotations using free text.
- compartment: Functional compartment for each cell type.
- manually_annotated: True or False, whether or not the corresponding value in Annotation has been manually verified by a tissue expert.
- method: smartseq2 (full-length) or 10x (3prime).
- n_counts_UMIs: number of counts (smartseq2) or UMIs (10x) per cell.
- n_genes: number of genes per cell.
The following numeric layers are available:
- .X: SpliZ values (column name ends with “_SpliZ”) as well as normalized and scaled decontX counts.
If you would like to interact further with the data, as e.g. finding a cell type specific splicing variant consider using exploratory-cellxgene.