DOI: 10.5061/dryad.zw3r228dh
title: Differentially-expressed genes in blood in response to lipopolysaccharide in three rodent species

description: Infection tolerance in rodents was examined by injecting single-dose
 lipopolysaccharide (LPS) to induce inflammation in Peromyscus
 leucopus (LL stock), the white-footed deermouse also reservoir
 for Lyme disease and Mus musculus (outbred CD-1 breed),
 the house mouse, and Rattus norvegicus, the brown rat (Fischer
 strain). Reaction to LPS was analyzed in the blood of challenged rodents
 and compared to control animals. As natural reservoirs of zoonoses
 deermice show significant anti-inflammatory response as described in
 "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). This project is a
 follow-up project focusing on the transcriptomic analysis of the whole
 blood bulk RNA-seq and further analysis of differentially expressed genes
 (DEG) between the treatment arm and controls. Complete fold change and
 false discovery rate for all three rodent species used for the current
 Dryad set are previously published (https://doi.org/10.7280/D1470Z). Here
 we report that deermice tolerance to infection is partly due to lower
 expression of interferon-gamma in comparison to mice and rats. 
description: <em>Peromyscus leucopus</em> (10 animals, 5 of each sex)
 and <em>M.
 musculus</em><em> </em>(10
 animals, 5 of each sex) were injected into the peritoneum with the
 solution of purified E. coli lipopolysaccharide (10
 microgram/gram of body weight). Same number of animals was injected with
 saline and used as controls. The rats were studied in a separate
 experiment with 5 control animals and 6 animals receiving 5 micrograms LPS
 per gram of body weight and 5 animals receiving 20 micrograms LPS per
 gram. All animals were euthanized 4 hours post-injection. Blood from each
 animal was used for extracting RNA and processed further using Novaseq
 Illumina technology with paired-end chemistry and 150 cycles for mice and
 deermice and 100 cycles for rats providing ~ 50 million reads per sample.
 After sequencing reads were trimmed and transcripts annotated using
 Genomics Workbench v. 23. Differential gene expression (DEG) was assessed
 using the same suite of software and a modification of EdgeR method.
 Sequenced data was deposited to National Center for
 Biotechnology Information (https://ncbi.nlm.nih.gov) BioProjects PRJNA975149 for the combined <em>P. leucopus </em>and<em> M. musculus</em> experiment (SRX20511260-SRX20511299), and PRJNA973677 for the <em>R. norvegicus</em> LPS experiment (SRX20509401-SRX20509416).
description: The data is in CSV tabular data format and can be opened as a
 text file or as a spreadsheet.
description: GENERAL INFORMATION * Title of Dataset: Differentially-expressed genes in
 Peromyscus leucopus, Mus musculus, and Rattus norvegicus blood in response
 to LPS * Author Information <br> A. Principal Investigator Contact
 Information <br> Name: Alan G. Barbour; Institution: University of
 California Irvine; Address: 843 Health Sciences Court, Irvine, CA 92697;
 Email: abarbour@uci.edu <br> B. Associate or Co-investigator Contact
 Information Name: Ana Milovic; Institution: University of California
 Irvine; Address: 843 Health Sciences Court, Irvine, CA 92697; Email:
 milovica@uci.edu * Date of data collection (single date, range,
 approximate date): 2017-2023 * Geographic location of data collection:
 Irvine, California, USA * Information about funding sources that supported
 the collection of the data: National Institute of Allergy and Infectious
 Diseases grants AI-136523 and AI-157513 SHARING/ACCESS INFORMATION 1.
 Licenses/restrictions placed on the data: None 2. Links to publications
 that cite or use the data: pending 3. Links to other publicly accessible
 locations of the data: Not applicable 4. Links/relationships to ancillary
 data sets: See below for BioProject numbers. 5. Was data derived from
 another source? yes/no <br> A. If yes, list source(s): No 6.
 Recommended citation for this dataset: The white-footed deermouse, an
 infection-tolerant reservoir for several zoonotic agents, tempers
 interferon responses to endotoxin in comparison to the mouse and rat,
 manuscript in preparation; preprint server DOI pending DATA & FILE
 OVERVIEW 1. File List: Table\_D1\_Pleucopus\_LPS\_RNAseq.csv
 Table\_D2\_Mmusculus\_LPS\_RNAseq.csv Table\_D3\_Pleucopus\_LPS\_DEG.csv
 Table\_D4\_Mmusculus\_LPS\_DEG.csv Table\_D5\_Pleucopus\_FvM\_DEG.csv
 Table\_D6\_Rnorvegicus\_LPS\_DEG.csv
 Table\_D7\_Pleu\_Mmus\_targetedLPS.csv 2. Relationship between files, if
 important: Not applicable 3. Additional related data collected that was
 not included in the current data package: The values for individual
 animals provided in Table\_D7\_Pleu\_Mmus\_targetedLPS.csv by species,
 sex, and treatment are provided in Supplementary Materials Table S2
 https://doi.org/10.7554/eLife.90135.1 4. Are there multiple versions of
 the dataset? No METHODOLOGICAL INFORMATION 1. Description of methods used
 for collection/generation of data: In brief, adult animals of the species
 Peromyscus leuopus LL stock, Mus musculus (CD-1 breed) or Rattus
 norvegicus Fischer strain were inoculated into the peritoneum (IP) with
 solution of purified E. coli lipopolysaccharide (10 microgram/gram body
 mass for P. leuocpus and M. musculus and 5 microgram or 20 microgram for
 R. norvegicus. Controls received saline alone. Four hours later animals
 were humanely euthanized and blood collected for complete blood count and
 for RNA extraction. 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). Details provided in
 article entitled "The white-footed deermouse, an infection-tolerant
 reservoir for several zoonotic agents, tempers interferon responses to
 endotoxin in comparison to the mouse and rat", manuscript in
 preparation; URL pending 2. Methods for processing the data: In brief,
 total RNA was extracted from whole blood and a stranded cDNA library was
 made. This was subjected Illumina sequencing with paired-ends and 150
 cycles. After quality control and trimming the reads were matched to
 current genome-wide transcript sets for reference genomes for P. leucopus.
 M. musculus, and R. norvegicus using CLC Genomics Workbench v. 23. The
 reads have been deposited with the NCBI SRA repository. Differential gene
 expression (DEG) was assessed using the same suite of software and a
 modification of EdgeR method. Sequenced data was deposited to National
 Center for Biotechnology Information (https://ncbi.nlm.nih.gov)
 BioProjects PRJNA975149 for the combined P. leucopus and M. musculus
 experiment (SRX20511260-SRX20511299), and PRJNA973677 for the R.
 norvegicus LPS experiment (SRX20509401-SRX20509416). 3. Instrument- or
 software-specific information needed to interpret the data: Not applicable
 4. Standards and calibration information, if appropriate: Control animals
 received endotoxin-free sterile saline, the diluent used for LPS, IP in
 the same volume during the same experiment. 5. Environmental/experimental
 conditions: see above 6. Describe any quality-assurance procedures
 performed on the data: Some samples were subjected to replicate cDNA
 library construction and separate sequencing positions in the flow cell.
 7. People involved with sample collection, processing, analysis and/or
 submission: Ana Milovic, Jonathan V. Duong, Vanessa J. Cook, and Alan G.
 Barbour DATA-SPECIFIC INFORMATION FOR:
 Table\_D1\_Pleucopus\_LPS\_RNAseq.csv 1. Number of variables: 20 2. Number
 of cases/rows: 54470 rows (including header) 3. Variable List: Variable
 List: transcript (NCBI species accession number), gene (gene name), animal
 (MM1-MM39 - animal ID, starting with letters MM referring to species),
 treatment (control or LPS), sex (male or female), TPM (each value is
 expressed in TPM) 4. Missing data codes: None 5. Specialized formats or
 other abbreviations used: None DATA-SPECIFIC INFORMATION FOR:
 Table\_D2\_Mmusculus\_LPS\_RNAseq.csv 1. Number of variables: 22 2. Number
 of cases/rows: 130333 rows (including header) 3. Variable List: transcript
 (NCBI species accession number), gene (gene name), animal (MM1-MM39 -
 animal ID, starting with letters MM referring to species), treatment
 (control or LPS), sex (male or female), TPM (each value is expressed in
 TPM) 4. Missing data codes: None 5. Specialized formats or other
 abbreviations used: None DATA-SPECIFIC INFORMATION FOR:
 Table\_D3\_Pleucopus\_LPS\_DEG.csv 1. Number of variables: 7 2. Number of
 cases/rows: 54467 rows (including header) 3. Variable List: accession
 (NCBI species accession number), gene (gene name), product (long gene
 name), maximum group mean (For each group in the statistical comparison,
 the average TPM is calculated. This value is the maximum of the average
 TPM's), length (gene length), fold-change (The (signed) fold change.
 Genes/transcripts that are not observed in any sample have undefined fold
 changes and are reported as NaN (not a number)), FDR (p-value The false
 discovery rate corrected p-value) 4. Missing data codes: None 5.
 Specialized formats or other abbreviations used: None DATA-SPECIFIC
 INFORMATION FOR: Table\_D4\_Mmusculus\_LPS\_DEG.csv 1. Number of
 variables: 7 2. Number of cases/rows: 130330 rows (including header) 3.
 Variable List: accession (NCBI species accession number), gene (gene
 name), product (long gene name), maximum group mean (For each group in the
 statistical comparison, the average TPM is calculated. This value is the
 maximum of the average TOM's), length (gene length), fold-change (The
 (signed) fold change. Genes/transcripts that are not observed in any
 sample have undefined fold changes and are reported as NaN (not a
 number)), FDR (p-value The false discovery rate corrected p-value) 4.
 Missing data codes: None 5. Specialized formats or other abbreviations
 used: None DATA-SPECIFIC INFORMATION FOR:
 Table\_D5\_Pleucopus\_FvM\_DEG.csv 1. Number of variables: 9 2. Number of
 cases/rows: 5013 rows (including header) 3. Variable List: transcript
 (NCBI species accession number), length (gene length, bases), gene (gene
 name), fem\_max (for each group in the statistical comparison, the average
 TPM is calculated. This value is the maximum of the average TPM's in
 females) fem\_log2 (The logarithmic fold change of fold change in
 females), fem\_FDR (the false discovery rate corrected p-value in
 females), male\_max (for each group in the statistical comparison, the
 average TPM is calculated. This value is the maximum of the average
 TPM's in males) male\_log2 (The logarithmic fold change of fold
 change in males), male\_FDR (the false discovery rate corrected p-value in
 males) 4. Missing data codes: None 5. Specialized formats or other
 abbreviations used: None DATA-SPECIFIC INFORMATION FOR:
 Table\_D6\_Rnorvegicus\_LPS\_DEG.csv 1. Number of variables: 7 2. Number
 of cases/rows: 99127 rows (including header) 3. Variable List: accession
 (NCBI species accession number), gene (gene name), product (long gene
 name), maximum group mean (For each group in the statistical comparison,
 the average TPM is calculated. This value is the maximum of the average
 TPM's), length (gene length), fold-change (The (signed) fold change.
 Genes/transcripts that are not observed in any sample have undefined fold
 changes and are reported as NaN (not a number)), FDR (p-value The false
 discovery rate corrected p-value) 4. Missing data codes: None 5.
 Specialized formats or other abbreviations used: None DATA-SPECIFIC
 INFORMATION FOR: Table\_D7\_Pleu\_Mmus\_targetedLPS.csv 1. Number of
 variables: 13 2. Number of cases/rows: 116 rows (including header) 3.
 Variable List: rank (Heatmap rank), gene (Gene name, the list includes the
 coding sequences listed in Methods of the manuscript and two endogenous
 retroviruses (ERV) proteins, Env and Gag-pol), Mus control mean (95% CI)
 (Mus control mean unique reads for the given gene normalized for reads for
 Ptprc (Cd45) gene for a sample. The 95% confidence intervals (CI) are
 asymmetric. Actual [gene]/Ptprc ratios are X 10^-3), Mus LPS mean (95% CI)
 (Mus LPS mean unique reads for the given gene normalized for reads for
 Ptprc (Cd45) gene for a sample. The 95% confidence intervals (CI) are
 asymmetric. Actual [gene]/Ptprc ratios are X 10^-3), Mus FC LPS vs control
 (Mus fold change post DEG analysis), Mus FDR p value (Mus p-value the
 false discovery rate corrected p-value), Peromyscus control mean (95% CI)
 (Peromyscuys control mean unique reads for the given gene normalized for
 reads for Ptprc (Cd45) gene for a sample. The 95% confidence intervals
 (CI) are asymmetric. Actual [gene]/Ptprc ratios are X 10^-3), Peromyscus
 LPS mean (95% CI) (Peromyscus LPS mean unique reads for the given gene
 normalized for reads for Ptprc (Cd45) gene for a sample. The 95%
 confidence intervals (CI) are asymmetric. Actual [gene]/Ptprc ratios are X
 10^-3), Peromyscus FC LPS v control (Peromyscus fold change post DEG
 analysis), Peromyscus FDR p-value (Peromyscus p-value the false discovery
 rate corrected p-value), Peromyscus v Mus control FC (Fold change post DEG
 analysis of Peromyscus vs. Mus controls), Peromyscus v Mus LPS FC (Fold
 change post DEG analysis of Peromyscus vs. Mus LPS), Peromyscus v Mus
 LPS/control (Fold change post DEG upregulated in LPS between species) 4.
 Missing data codes: None 5. Specialized formats or other abbreviations
 used: None