All the raw and curated data is provided for download below.
Raw sequence data is deposited as .bam files in the sequence read archive under accession SRP135960, available at https://www.ncbi.nlm.nih.gov/sra/SRP135960.
Useful if you want to reanalyze everything from scratch. Note that these .bam files are output files from the cellranger pipeline; The original cellular index is available in the CR tag and the UMI in the UR tag.Available as a single file l5_all_rev1.loom (barcodes revised), with one cell per column and one gene per row. Metadata is available as row and column attributes.
Suitable for exploring single cells. Note that there was an issue with the original file in which many samples had their barcode truncated with two bases at the 5' end. The revised loom file above has corrected all cases where the correct barcode can be uniquely matched. In 797 cases the matching is not unique and the two 5' bases have been set to 'XX'. For the original loom file without corrections: l5_all.loomAvailable as a single file L5_All.agg.loom, with one cluster per column and one gene per row. Metadata is available as row and column attributes.
Suitable for exploring cell types.Note: expression data is provided in Loom format. See loompy.org to learn how to work with Loom files from your favourite programming language.
Subsets of data are also available as loom files here: