Question: Do you have the cell-type annotations for the 1.3 million mouse brain cells dataset?
Answer: 10x Genomics does not provide the annotations of the 1.3M mouse brain cell data set as a resource. The objective was to share the dataset as-is with the research community for more detailed analysis and curation:
The whole genome transcriptome data for 1.3 million murine brain cells is open to the research community for method development and biological discovery.
In the related application note, an exploratory analysis of a subset of 20,000 cells was briefly highlighted with some putative annotations based on clustering, gene-marker enrichment, and comparison to reference transcriptomes (1).
Annotations of cell-types are an active area of research and the preliminary classifications in the application note and website are not expected to be comprehensive.
The much smaller data 20K cell matrix (58MB) is also available for download from the dataset site:
- Description: "matrix of sampled 20k cells" contains the filtered gene-cell-barcode matrix of a randomly sampled 20k cells. This file can be opened in R using the function
get_matrix_from_h5in the Cell Ranger: R Kit. - Download Link
This might be more tractable for initial annotation and exploration.
(1) Tasic et al. Nat Neurosci. 2016 Feb;19(2):335-46.