DOI: 10.7280/d1470z
title: In vivo differentially-expressed genes in Peromyscus leucopus, Mus musculus, and Rattus norvegicus blood in response to LPS

description: Animals that are competent reservoirs of zoonotic pathogens commonly
 suffer little morbidity or apparent pathology from the infections. To
 investigate mechanisms of this tolerance of infection, we used single-dose
 lipopolysaccharide (LPS) as an experimental model of inflammation and
 compared the four hour post-injection responses by three rodents: the
 cricetine rodent Peromyscus leucopus (LL stock), the white-footed
 deermouse and reservoir for agents of Lyme disease and other zoonoses, and
 the murids Mus musculus (outbred CD-1 breed), the house mouse, and Rattus
 norvegicus, the brown rat (Fischer strain). The data presented here are
 part of a follow-up study of this phenomenon that was previoiusly reported
 with the title "An Infection-Tolerant Mammalian Reservoir for Several
 Zoonotic Agents Broadly Counters the Inflammatory Effects of
 Endotoxin" (https://doi.org/10.1128/mBio.00588-21). The project and
 the description of the samples are described under the following NCBI
 BioProjects:PRJNA975149
 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA975149) for mouse
 and deermouse and PRJNA973677
 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA973677). The manuscript
 associated with the accompanying data of this follow-up study is in
 preparation. The basic experimental design (described below) is the same
 as for the prior study: a genome-wide RNA-seq of whole blood using
 reference transcript set and then an analysis for differential gene
 expression (DEG) between LPS-treated animals and controls for each of the
 species. The accompanying dataset comprises the DEGs for deermice, mice,
 and rats in this study. There were multiple differences in the rankings of
 the DEGs by lowest p value between species with the greatest number of
 differences between P. leucopus, which is in the familly Cricetidae, and
 the mice and rats, which are in the family Muridae. Overall, the deermice
 in the study displayed a greater anti-inflammatory response than the mice
 and rats in the study. An example was interferon-gamma (Ifng) which was
 one of the top ranked DEGs for the mice and rats but not for the deermice.
description: Adult animals of the species <em>Peromyscus
 leuopus</em> LL stock, <em>Mus musculus</em> (CD-1
 breed) or <em>Rattus norvegicus</em> Fischer strain were
 inoculated into the peritoneum (IP) with solution of purified <em>E.
 coli</em> lipopolysaccharide (10 microgram/gram body mass for
 <em>P. leuocpus</em> and <em>M. musculus</em> and
 5 microgram or 20 microgram for <em>R. norvegicus</em>.
 Controls received saline alone. <em>P. leucopus</em> and
 <em>M. musculus</em> were in the same experiment and there
 were 10 animals (5 of each sex) in the treatment group and 10 animals (5
 of each sex) in the control group. The rats were studied in a separate
 experiment with 5 control animals and 6 animals receiving 5 microgram LPS
 per gram and 5 animals receiving 20 micrograms LPS per gram. In both
 experiments 4 hours after LPS or control injections the animals were
 humanely euthanized and blood collected for complete blood count and for
 RNA extraction. The extracte RNA was subjected to stranded cDNA library
 preparation and then Illumina technology (Novaseq) as described in https://doi.org/10.1128/mBio.00588-21 with paired-end sequencing chemistry and 150 cycles for the deermouse and mouse samples and 100 cycles for the rat samples. There were an average of ~50 million reads per sample. After quality control and trimming the reads were matched to current genome-wide transcript sets for reference genomes for <em>P. leucopus. M. musculus</em>, and <em>R. norvegicus</em> using CLC Genomics Workbench v. 23. Differential gene expression (DEG) was assessed using the same suite of software and a modification of EdgeR method. The genes listed in the table had false discovery rate p values of less than 0.05 and fold-changes up or down of greater than 1.5X.
description: The data is in CSV tabular data format and can be opened as a
 text file or as a spreadsheet.