Note: This section is adapted from the assignments provided to us by the Harvard CCB liaison team.
Recreate a part of the SummarizedExperiment paradigm for storing and representing gene expression data in a relational database setting by linking two data tables (expression data and cell metadata).
Obtain the segmented expression data from the MERFISH mouse hypothalamus dataset from DataDryad. Divide the obtained csv file into 1) columns storing expression levels of individual genes, and 2) cell metadata such as animal ID, animal sex, and cell class. Create a SQL table for both data components, with the two tables being linked by the cell ID. Perform a number of select queries to obtain eg. a) all cells of a certain cell type, b) all cells of female mice, and c) all pericytes with non-zero expression of the Ace2 gene.
The segmented expression data can be downloaded from datadryad.
Just run our companion notebook Assignment3Notebook.ipynb!