Chapter 17 About the Data

17.1 10X Genomics PBMC Data

The TENxPBMCData package provides a Bioconductor resource for representing and manipulating nine different single-cell RNA-seq (scRNA-seq) data sets on peripheral blood mononuclear cells (PBMC) generated by 10X Genomics from various healthy donors. Here we generally make use of the smaller datasets, pbmc3k and pbmc4k, available via the package. For more information, we refer to the 10X Genomics datasets online resource (PBMC data is within the Single Cell Gene Expression table).

17.2 Cellbench_data

The 5 cell line scRNA-seq data from the CellBench_data repository is used in examples where having a cell label is important. In the CellBench_data repository, the data is stored within the workspace data/sincell_with_class_5cl.RData as sc_10x_5cl_qc. We have extracted it and saved it under this book’s Github repo within the _rfiles/_data folder for ease of use.

The data arrives as a SingleCellExperiment class object, and has already undergone basic preprocessing, including quality control and normalization. The most important aspect to this data - the cell labels pertaining to the 5 cell lines sequenced - can be found within the colData component under the column name cell_line.

Note that this data will be made available on Bioconductor via the scRNAseq package in the near future.