Host nasopharyngeal transcriptome dataset of a SARS-CoV-2 positive Italian cohort

The ongoing COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people worldwide and has significant implications for public health. Host transcriptomics profiling provides comprehensive understanding of how the virus interacts with host cells and how the host responds to the virus. COVID-19 disease alters the host transcriptome, affecting cellular pathways and key molecular functions. 

To contribute to the global effort to understand the virus’s effect on host cell transcriptome, we have generated a dataset from nasopharyngeal swabs of 35 individuals infected with SARS-CoV-2 from the Campania region in Italy during the three outbreaks, with different clinical conditions. This dataset will help to elucidate the complex interactions among genes and can be useful in the development of effective therapeutic pathways.

• File_1 contains the  list of differentially expressed genes obtained comparing patients of I vs III period.
• File_2 contains the raw counts for each gene in each sample.
• File_3 contains the List of Canonical Pathways involving differentially expressed genes 
• File_4 contains the  R code used for differential expression analysis
• File_5 contains the List of Canonical Pathways involving differentially expressed genes. For each pathway the following information are provided: Number of genes involved in the  function, according IPA(column D), Number of differentially expressed genes involved in that function (column E), Number of genes, belonging to that function, but not overlapping with DE ones (column F)