Transcriptomics dataset

We selected the following publicly available RNA-seq dataset as an example for workshop days 2-3:

• Primary human lung epithelium (NHBE cells) were mock treated or infected with SARS-CoV-2 (USA-WA1/2020).
• The dataset has been uploaded to GEO - identifier: GSE147507.
• The dataset was used in the publications by Blanco-Melo D. et. al. in 2020 (doi: 10.1016/j.cell.2020.04.026).
• The dataset looks at different cell lines and exposures. In the workshop, we will focus on Series1 NHBE_SARS-CoV-2 vs. NHBE_Mock.

Pre-processing and differential analysis

• The pre-processing and statistical anslysis was done with DESeq2 in R (see script here).
• 21,207 genes were measured.

• 1,333 genes are differentially expressed (p-value < 0.05,

  log2FC

  > 0.26)