title: Analytical workflow profiling gene expression in murine macrophages.
abstract: Comprehensive and simultaneous analysis of all genes in a biological sample is a capability of RNA-Seq technology. Analysis of the entire transcriptome benefits from summarization of genes at the functional level. As a cellular response of interest not previously explored with RNA-Seq, peritoneal macrophages from mice under two conditions (control and immunologically challenged) were analyzed for gene expression differences. Quantification of individual transcripts modeled RNA-Seq read distribution and uncertainty (using a Beta Negative Binomial distribution), then tested for differential transcript expression (False Discovery Rate-adjusted p-value < 0.05). Enrichment of functional categories utilized the list of differentially expressed genes. A total of 2079 differentially expressed transcripts representing 1884 genes were detected. Enrichment of 92 categories from Gene Ontology Biological Processes and Molecular Functions, and KEGG pathways were grouped into 6 clusters. Clusters included defense and inflammatory response (Enrichment Score = 11.24) and ribosomal activity (Enrichment Score = 17.89). Our work provides a context to the fine detail of individual gene expression differences in murine peritoneal macrophages during immunological challenge with high throughput RNA-Seq.
authors.affiliation: Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Nixon
authors.forename: Dianelys
authors.initials: D
authors.lastname: González-Peña
authors.forename: Marcus A
authors.initials: MA
authors.lastname: Lawson
authors.forename: Robert H
authors.initials: RH
authors.lastname: McCusker
authors.forename: Alvaro G
authors.initials: AG
authors.lastname: Hernandez
authors.forename: Jason C
authors.initials: JC
authors.lastname: O'Connor
authors.forename: Robert
authors.initials: R
authors.lastname: Dantzer
authors.forename: Keith W
authors.initials: KW
authors.lastname: Kelley
authors.forename: Sandra L
authors.initials: SL
authors.lastname: Rodriguez-Zas
mesh_terms: D000818:Animals; D019295:Computational Biology; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D063990:Gene Ontology / Q000706:statistics & numerical data; D017737:Macrophages, Peritoneal / Q000276:immunology / Q000378:metabolism*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D017423:Sequence Analysis, RNA / Q000706:statistics & numerical data; D057188:Workflow
keywords: RNA-Seq; functional analysis; macrophage; transcriptome