Dataset walkthrough
These cellxgene sessions enable you to explore and reannotate the data interactively using the browser. Cells are displayed in an FIRM integrated UMAP according to the overall transcriptional similarity.
The cellxgene portal also allows visualization of gene expression by searching the gene symbol in the “Genes” search box. Gene expression can be visualized as a gradient-colored scatter plot of the cell UMAP (by clicking the color button next to the gene). Color gradient represents the cellular expression of the selected gene. Expression levels are after library size normalization and natural log transformation (i.e., smartseq2, ln(reads/N *1e4 +1); 10x, ln(UMI/N *1e4 +1), where N denotes the total number of reads or UMI of the cell).
The following metadata categories are available for the cells sequenced:
- nCount_RNA: number of total reads (smartseq2) or UMI (10x).
- nFeature_RNA: number of genes per cell.
- method: smartseq2 (full-length) or 10x (3prime).
- individual: lemur individuals available in the dataset.
- age: age of the individual (years).
- sex: sex of the individual.
- tissue: tissue sampled.
- subtissue: specification of the anatomical site sampled within the tissue. For tissues sampled multiple times at the same anatomical site, each 10x channel has distinct subtissue number.
- compartment_v1: functional compartment for each cell type (i.e., epithelial, endothelial, stromal, immune (hematopoietic, lymphoid, myeloid, megakaryocyte-erythroid), neural, germ).
- cell_ontology_class_v1: cell type designation using the Cell Ontology.
- free_annotation_v1: detailed cell type designation using free text and molecular markers. PF, proliferating; LQ, low quality.
- dendrogram_annotation_number: number assigned to each of the 256 cell type designations across the Tabula Microcebus, arranged by compartment and then ordered by organ system or biological relatedness (according to Fig. 2A in Tabula Microcebus manuscript). In addition, separate numbering is assigned to each of hybrid and mix cell types (labeled with prefix letter ‘H’ and ‘M’, respectively).
- MHC: counts for the major histocompatibility complex (MHC) genes based on reannotation of the locus using expression data from the Tabula Microcebus (original locus annotation from NCBI’s Annotation Release 101). Note the count is only available for cells sequenced by 10x method and count is NAN for cells sequenced by smartseq2 method. nMHC_C_I, sum of normalized counts from classical Class I genes (Mimu-168, -W03, -W04, -249); nMHC_NC_I, non-classical Class I genes (Mimu-180ps, -191, -202, -208, -218, -229ps, -239ps) and nMHC_all_II, Class II genes (Mimu- DMA, DMB, DPA, DPB, DQA, DQB, DRA, DRB). Separate counts for each gene available in h5ad files on Figshare, with both raw counts and normalized counts (labeled with prefix letter ‘n’) provided.
H5ad files with full list of metadata categories and numeric layers (raw and normalized counts) available on FigShare. The data is organized as described in the data tab.
You will find below a link for each organ available in Tabula Microcebus. If you would like to contribute additional annotations please use this button to complete the required google form.
