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