Dataset walkthrough

These cellxgene sessions enable you to reannotate the data using the browser.

The following metadata categories are available:

  • method: smartseq2 (full-length) or 10x (3prime).
  • individual: lemur individuals available in the dataset. For details see the lemur characteristics summary.
  • sex: sex of individuals.
  • age: age of individuals (years).
  • subtissue: list of subtissues available in the dataset.
  • compartment_v1: functional compartment for each cell type.
  • cell_ontology_class_v1: cell type annotations using the Cell Ontology.
  • free_annotation_v1: detailed cell type annotations using free text and molecular markers. PF, proliferating; LQ, low quality.
  • nCount_RNA: number of normalized counts (smartseq2, ln(reads/N *1e4 +1)) or UMIs (10x, ln(UMI/N *1e4 +1)) per cell.
  • nFeature_RNA: number of genes per cell.
  • 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). In cellxgene: 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 (n-prefix).

The following numeric layers are available in h5ad file on FigShare:

  • raw_counts: raw, raw, not normalized counts.
  • .X normalized, not scaled, counts (smartseq2, ln(reads/N *1e4 +1); 10x, ln(UMI/N *1e4 +1)).

You will find below a link for each organ available in Tabula Microcebus. If you would like to contribute please use this button to complete the required google form.

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Per Tissue Objects