Preprocessing of Public RNA-Sequencing Datasets to Facilitate Downstream Analyses of Human Diseases

Rapier-Sharman, Naomi Krapohl John Beausoleil Ethan J.; Gifford, Kennedy T. L.; Hinatsu, Benjamin R.; Hoffmann, Curtis S.; Komer, Makayla Scott Tiana M.; Pickett, Brett E.

Publicly available RNA-sequencing (RNA-seq) data are a rich resource for elucidating the mechanisms of human disease;however, preprocessing these data requires considerable bioinformatic expertise and computational infrastructure. Analyzing multiple datasets with a consistent computational workflow increases the accuracy of downstream meta-analyses. This collection of datasets represents the human intracellular transcriptional response to disorders and diseases such as acute lymphoblastic leukemia (ALL), B-cell lymphomas, chronic obstructive pulmonary disease (COPD), colorectal cancer, lupus erythematosus;as well as infection with pathogens including Borrelia burgdorferi, hantavirus, influenza A virus, Middle East respiratory syndrome coronavirus (MERS-CoV), Streptococcus pneumoniae, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We calculated the statistically significant differentially expressed genes and Gene Ontology terms for all datasets. In addition, a subset of the datasets also includes results from splice variant analyses, intracellular signaling pathway enrichments as well as read mapping and quantification. All analyses were performed using well-established algorithms and are provided to facilitate future data mining activities, wet lab studies, and to accelerate collaboration and discovery.