Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia.

ABSTRACT: Thousands of Pseudomonas aeruginosa RNA sequencing (RNA-seq) gene expression profiles are publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). In this work, the transcriptional profiles from hundreds of studies performed by over 75 research groups were reanalyzed in aggregate to create a powerful tool for hypothesis generation and testing. Raw sequence data were uniformly processed using the Salmon pseudoaligner, and this read mapping method was validated by comparison to a direct alignment method. We developed filtering criteria to exclude samples with aberrant levels of housekeeping gene expression or an unexpected number of genes with no reported values and normalized the filtered compendia using the ratio-of-medians method. The fi

SUBMITTER: Doing G 

PROVIDER: S-EPMC9948711 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature