CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies

• Published in: Scientific data 2022-06, Vol.9 (1), p.343-343, Article 343
• Main Authors: Neff, Samuel L., Hampton, Thomas H., Puerner, Charles, Cengher, Liviu, Doing, Georgia, Lee, Alexandra J., Koeppen, Katja, Cheung, Ambrose L., Hogan, Deborah A., Cramer, Robert A., Stanton, Bruce A.
• Format: Article
• Language: English
• Subjects: 631/114/2401; 631/1647/2017; Computer applications; Cystic fibrosis; Cystic Fibrosis - genetics; Data Analysis; Gene expression; Humanities and Social Sciences; Humans; multidisciplinary; Pathogens; RNA-Seq; Science; Science (multidisciplinary); Sequence Analysis, RNA; Software
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/s41597-022-01431-1

Researchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and manual effort are required to compare similar studies, visualize gene expression patterns within studies, and use published data to generate new experimental hypotheses. Furthermore, it is difficult to filter available studies by domain-relevant attributes such as strain, treatment, or media, or for a researcher to assess how a specific gene responds to various experimental conditions across studies. To reduce these barriers to data re-analysis, we have developed an R Shiny application called CF-Seq, which works with a compendium of 128 studies and 1,322 individual samples from 13 clinically relevant CF pathogens. The application allows users to filter studies by experimental factors and to view complex differential gene expression analyses at the click of a button. Here we present a series of use cases that demonstrate the application is a useful and efficient tool for new hypothesis generation. (CF-Seq: http://scangeo.dartmouth.edu/CFSeq/ )