Single Cell data for "Prospective isolation and single cell profiling of NKX2-1+/CD47+ human lung progenitors derived from pluripotent stem cells"

The data and associated scripts that were used to create the single cell figures in the paper "Prospective isolation and single cell profiling of NKX2-1+/CD47+ human lung progenitors derived from pluripotent stem cells"

Interactive version of the monocle data can be found here: https://iandriver.shinyapps.io/ips17-bu3_single_cell_data/

Instructions

Clone or download this repository and move working directory there:

    git clone https://github.com/iandriver/ips17-BU3-single-cell.git
    cd ips17-BU3-single-cell

or if working in RStudio:

    setwd('path_to/ips17-BU3-single-cell')

Then run the script "monocle2_ips17_BU3.R".

    Rscript monocle2_ips17_BU3.R

or run in in RStudio.

This will rerun the analysis, but the pseudotime ordering is non-dimensional, so the resulting monocle object may be reversed. Rerun these two commands to flip the trajectory until it is correct:

    ips17_BU3_data <- reduceDimension(ips17_BU3_data, max_components=3)
    ips17_BU3_data <- orderCells(ips17_BU3_data, reverse=TRUE)

Or simply load the existing monocle CellDataSet:

    ips17_BU3_data <- readRDS('kmeans2_new_allgene200.RDS')

This can then be used for any plotting or analysis. Simple interactive plotting of this data can also be found here: https://iandriver.shinyapps.io/ips17-bu3_single_cell_data/