team_bdf

The R markdown file commited into the repository. The data for this R markdown file comes from a Nature Cell Biology paper, EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival (Fu et al. 2015). Both the raw data (sequence reads) and processed data (counts) can be downloaded from Gene Expression Omnibus database (GEO) under accession number GSE60450.

This study examines the expression profiles of basal stem-cell enriched cells (B) and committed luminal cells (L) in the mammary gland of virgin, pregnant and lactating mice. Six groups are present, with one for each combination of cell type and mouse status. Each group contains two biological replicates. We will first use the counts file as a starting point for our analysis.

Reference links:

1. http://www.statsci.org/smyth/pubs/QLedgeRPreprint.pdf
2. http://monashbioinformaticsplatform.github.io/RNAseq-DE-analysis-with-R/RNAseq_DE_analysis_with_R.html
3. https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html#Introduction_and_data_import =