GENERAL INFORMATION

1. Title of Dataset: Transcriptome of Peromyscus leucopus brain and lungs infected with SARS-CoV-2 

2. Author Information

  A. Principal Investigator Contact Information

  Name: Alan G. Barbour

  Institution: University of California Irvine

  Address: 843 Health Sciences Court, Irvine, CA 92697

  Email: abarbour@uci.edu

  B. Associate or Co-investigator Contact Information

  Name: Ana Milovic

  Institution: University of California Irvine

  Address: 843 Health Sciences Court, Irvine, CA 92697

  Email: anamilovic@gmail.com

3. Date of data collection (single date, range, approximate date): 2020-2022

4. Geographic location of data collection: Irvine, California, USA

5. Information about funding sources that supported the collection of the data: National Institute of Allergy and Infectious Diseases grant AI-136523

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

  A. If yes, list source(s): No

6. Recommended citation for this dataset: https://doi.org/10.64898/2026.03.13.711660

DATA & FILE OVERVIEW

1. File List: TPM_UGR.xlsx

2. Relationship between files, if important: This data is used for subsequent study to calculate DEGs published under https://doi.org/10.5061/dryad.9ghx3ffzn

3. Additional related data collected that was not included in the current data package: None

4. Are there multiple versions of the dataset? No

METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: Peromyscus leucopus is a reservoir for numerous zoonoses and one of the most abundant mammals in North America. Since they live near humans we are interested in the possibility of SARS-CoV-2 infection in this animal model from a zoonoses standpoint. P. leucopus were experimentally inoculated intranasally with either tissue culture medium (DMEM) as controls or SARS-CoV-2 (WA1 strain, alpha variant) at a dose of 2 × 10⁴. Animals were euthanized at 3 or 6 days post-infection. Lung and brain tissues were collected for RNA isolation. Total RNA was extracted, and RNA-seq libraries were prepared and sequenced using high-throughput platforms. Raw reads were processed and aligned to the reference P. leucopus coding DNA sequence (CDS). Gene expression was quantified and normalized to generate Transcripts Per Million (TPM) and Unique Gene Reads (UGR) values for each gene.

2. Instrument- or software-specific information needed to interpret the data: Not applicable

3. Standards and calibration information, if appropriate: NA

4. Environmental/experimental conditions: see above

5. 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.

6. People involved with sample collection, processing, analysis and/or submission: Ana Milovic, Alan G. Barbour

DATA-SPECIFIC INFORMATION FOR: Lung_pero_CDS_UGR

1. Number of variables: 31

2. Number of cases/rows: 22669 rows (including header)

3. Variable List: Gene_Name (gene symbol or identifier corresponding to each row in the gene expression count matrix), PL25117_3_V_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25117 collected 3 days post-infection from a virus-infected male animal in experiment 1), PL25130_3_V_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25130 collected 3 days post-infection from a virus-infected male animal in experiment 1), PL25013_3_V_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25013 collected 3 days post-infection from a virus-infected female animal in experiment 1), PL25025_3_V_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25025 collected 3 days post-infection from a virus-infected female animal in experiment 1), PL25255_3_V_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25255 collected 3 days post-infection from a virus-infected male animal in experiment 2), PL25165_3_V_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25165 collected 3 days post-infection from a virus-infected male animal in experiment 2), PL25298_3_V_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25298 collected 3 days post-infection from a virus-infected female animal in experiment 2), PL25304_3_V_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25304 collected 3 days post-infection from a virus-infected female animal in experiment 2), PL25161_6_V_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25161 collected 6 days post-infection from a virus-infected male animal in experiment 1), PL25157_6_V_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25157 collected 6 days post-infection from a virus-infected male animal in experiment 1), PL25158_6_V_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25158 collected 6 days post-infection from a virus-infected female animal in experiment 1), PL25128_6_V_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25128 collected 6 days post-infection from a virus-infected female animal in experiment 1), PL25136_6_V_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25136 collected 6 days post-infection from a virus-infected male animal in experiment 2), PL25163_6_V_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25163 collected 6 days post-infection from a virus-infected male animal in experiment 2), PL25228_6_V_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25228 collected 6 days post-infection from a virus-infected female animal in experiment 2), PL25306_6_V_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25306 collected 6 days post-infection from a virus-infected female animal in experiment 2), PL25124_3_C_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25124 collected 3 days post-infection from a control male animal in experiment 1), PL25160_3_C_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25160 collected 3 days post-infection from a control female animal in experiment 1), PL25169_3_C_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25169 collected 3 days post-infection from a control male animal in experiment 1), PL25281_3_C_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25281 collected 3 days post-infection from a control male animal in experiment 2), PL25152_3_C_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25152 collected 3 days post-infection from a control male animal in experiment 2), PL25225_3_C_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25225 collected 3 days post-infection from a control female animal in experiment 2), PL25226_3_C_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25226 collected 3 days post-infection from a control female animal in experiment 2), PL25159_6_C_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25159 collected 6 days post-infection from a control male animal in experiment 1), PL25018_6_C_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25018 collected 6 days post-infection from a control female animal in experiment 1), PL25167_6_C_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25167 collected 6 days post-infection from a control female animal in experiment 1), PL25280_6_C_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25280 collected 6 days post-infection from a control male animal in experiment 2), PL25287_6_C_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25287 collected 6 days post-infection from a control male animal in experiment 2), PL25313_6_C_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25313 collected 6 days post-infection from a control female animal in experiment 2), PL25219_6_C_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25219 collected 6 days post-infection from a control female animal in experiment 2).

4. Missing data codes: None

5. Specialized formats or other abbreviations used: None

DATA-SPECIFIC INFORMATION FOR: Lung_pero_CDS_TPM

1. Number of variables: 31

2. Number of cases/rows: 22669 rows (including header)

3. Variable List: Gene_Name (gene symbol or identifier corresponding to each row in the gene expression matrix), PL25117_3_V_M_E1.TPM (transcripts per million for sample PL25117 collected 3 days post-infection from a virus-infected male animal in experiment 1), PL25130_3_V_M_E1.TPM (transcripts per million for sample PL25130 collected 3 days post-infection from a virus-infected male animal in experiment 1), PL25013_3_V_F_E1.TPM (transcripts per million for sample PL25013 collected 3 days post-infection from a virus-infected female animal in experiment 1), PL25025_3_V_F_E1.TPM (transcripts per million for sample PL25025 collected 3 days post-infection from a virus-infected female animal in experiment 1), PL25255_3_V_M_E2.TPM (transcripts per million for sample PL25255 collected 3 days post-infection from a virus-infected male animal in experiment 2), PL25165_3_V_M_E2.TPM (transcripts per million for sample PL25165 collected 3 days post-infection from a virus-infected male animal in experiment 2), PL25298_3_V_F_E2.TPM (transcripts per million for sample PL25298 collected 3 days post-infection from a virus-infected female animal in experiment 2), PL25304_3_V_F_E2.TPM (transcripts per million for sample PL25304 collected 3 days post-infection from a virus-infected female animal in experiment 2), PL25124_3_C_M_E1.TPM (transcripts per million for sample PL25124 collected 3 days post-infection from a control male animal in experiment 1), PL25160_3_C_F_E1.TPM (transcripts per million for sample PL25160 collected 3 days post-infection from a control female animal in experiment 1), PL25169_3_C_M_E1.TPM (transcripts per million for sample PL25169 collected 3 days post-infection from a control male animal in experiment 1), PL25281_3_C_M_E2.TPM (transcripts per million for sample PL25281 collected 3 days post-infection from a control male animal in experiment 2), PL25152_3_C_M_E2.TPM (transcripts per million for sample PL25152 collected 3 days post-infection from a control male animal in experiment 2), PL25225_3_C_F_E2.TPM (transcripts per million for sample PL25225 collected 3 days post-infection from a control female animal in experiment 2), PL25226_3_C_F_E2.TPM (transcripts per million for sample PL25226 collected 3 days post-infection from a control female animal in experiment 2), PL25159_6_C_M_E1.TPM (transcripts per million for sample PL25159 collected 6 days post-infection from a control male animal in experiment 1), PL25018_6_C_F_E1.TPM (transcripts per million for sample PL25018 collected 6 days post-infection from a control female animal in experiment 1), PL25167_6_C_F_E1.TPM (transcripts per million for sample PL25167 collected 6 days post-infection from a control female animal in experiment 1), PL25280_6_C_M_E2.TPM (transcripts per million for sample PL25280 collected 6 days post-infection from a control male animal in experiment 2), PL25287_6_C_M_E2.TPM (transcripts per million for sample PL25287 collected 6 days post-infection from a control male animal in experiment 2), PL25313_6_C_F_E2.TPM (transcripts per million for sample PL25313 collected 6 days post-infection from a control female animal in experiment 2), PL25219_6_C_F_E2.TPM (transcripts per million for sample PL25219 collected 6 days post-infection from a control female animal in experiment 2), PL25161_6_V_M_E1.TPM (transcripts per million for sample PL25161 collected 6 days post-infection from a virus-infected male animal in experiment 1), PL25157_6_V_M_E1.TPM (transcripts per million for sample PL25157 collected 6 days post-infection from a virus-infected male animal in experiment 1), PL25158_6_V_F_E1.TPM (transcripts per million for sample PL25158 collected 6 days post-infection from a virus-infected female animal in experiment 1), PL25128_6_V_F_E1.TPM (transcripts per million for sample PL25128 collected 6 days post-infection from a virus-infected female animal in experiment 1), PL25136_6_V_M_E2.TPM (transcripts per million for sample PL25136 collected 6 days post-infection from a virus-infected male animal in experiment 2), PL25163_6_V_M_E2.TPM (transcripts per million for sample PL25163 collected 6 days post-infection from a virus-infected male animal in experiment 2), PL25228_6_V_F_E2.TPM (transcripts per million for sample PL25228 collected 6 days post-infection from a virus-infected female animal in experiment 2), PL25306_6_V_F_E2.TPM (transcripts per million for sample PL25306 collected 6 days post-infection from a virus-infected female animal in experiment 2).

4. Missing data codes: None

5. Specialized formats or other abbreviations used: None

DATA-SPECIFIC INFORMATION FOR: Brain_pero_CDS_UGR

1. Number of variables: 31

2. Number of cases/rows: 22669 rows (including header)

3. Variable List: Gene_Name (gene symbol or identifier corresponding to each row in the gene expression count matrix), PL25117_3_V_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25117 collected 3 days post-infection from a virus-infected male animal in experiment 1), PL25130_3_V_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25130 collected 3 days post-infection from a virus-infected male animal in experiment 1), PL25013_3_V_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25013 collected 3 days post-infection from a virus-infected female animal in experiment 1), PL25025_3_V_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25025 collected 3 days post-infection from a virus-infected female animal in experiment 1), PL25255_3_V_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25255 collected 3 days post-infection from a virus-infected male animal in experiment 2), PL25165_3_V_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25165 collected 3 days post-infection from a virus-infected male animal in experiment 2), PL25298_3_V_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25298 collected 3 days post-infection from a virus-infected female animal in experiment 2), PL25304_3_V_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25304 collected 3 days post-infection from a virus-infected female animal in experiment 2), PL25161_6_V_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25161 collected 6 days post-infection from a virus-infected male animal in experiment 1), PL25157_6_V_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25157 collected 6 days post-infection from a virus-infected male animal in experiment 1), PL25158_6_V_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25158 collected 6 days post-infection from a virus-infected female animal in experiment 1), PL25128_6_V_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25128 collected 6 days post-infection from a virus-infected female animal in experiment 1), PL25136_6_V_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25136 collected 6 days post-infection from a virus-infected male animal in experiment 2), PL25163_6_V_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25163 collected 6 days post-infection from a virus-infected male animal in experiment 2), PL25228_6_V_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25228 collected 6 days post-infection from a virus-infected female animal in experiment 2), PL25306_6_V_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25306 collected 6 days post-infection from a virus-infected female animal in experiment 2), PL25124_3_C_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25124 collected 3 days post-infection from a control male animal in experiment 1), PL25160_3_C_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25160 collected 3 days post-infection from a control female animal in experiment 1), PL25169_3_C_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25169 collected 3 days post-infection from a control male animal in experiment 1), PL25281_3_C_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25281 collected 3 days post-infection from a control male animal in experiment 2), PL25152_3_C_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25152 collected 3 days post-infection from a control male animal in experiment 2), PL25225_3_C_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25225 collected 3 days post-infection from a control female animal in experiment 2), PL25226_3_C_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25226 collected 3 days post-infection from a control female animal in experiment 2), PL25159_6_C_M_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25159 collected 6 days post-infection from a control male animal in experiment 1), PL25018_6_C_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25018 collected 6 days post-infection from a control female animal in experiment 1), PL25167_6_C_F_E1.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25167 collected 6 days post-infection from a control female animal in experiment 1), PL25280_6_C_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25280 collected 6 days post-infection from a control male animal in experiment 2), PL25287_6_C_M_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25287 collected 6 days post-infection from a control male animal in experiment 2), PL25313_6_C_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25313 collected 6 days post-infection from a control female animal in experiment 2), PL25219_6_C_F_E2.Unique.gene.reads (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25219 collected 6 days post-infection from a control female animal in experiment 2).

4. Missing data codes: None

5. Specialized formats or other abbreviations used: None

DATA-SPECIFIC INFORMATION FOR: Brain_pero_CDS_TPM

1. Number of variables: 31

2. Number of cases/rows: 22669 rows (including header)

3. Variable List: Gene_Name (gene symbol or identifier corresponding to each row in the gene expression matrix), PL25117_3_V_M_E1.TPM (transcripts per million for sample PL25117 collected 3 days post-infection from a virus-infected male animal in experiment 1), PL25130_3_V_M_E1.TPM (transcripts per million for sample PL25130 collected 3 days post-infection from a virus-infected male animal in experiment 1), PL25013_3_V_F_E1.TPM (transcripts per million for sample PL25013 collected 3 days post-infection from a virus-infected female animal in experiment 1), PL25025_3_V_F_E1.TPM (transcripts per million for sample PL25025 collected 3 days post-infection from a virus-infected female animal in experiment 1), PL25255_3_V_M_E2.TPM (transcripts per million for sample PL25255 collected 3 days post-infection from a virus-infected male animal in experiment 2), PL25165_3_V_M_E2.TPM (transcripts per million for sample PL25165 collected 3 days post-infection from a virus-infected male animal in experiment 2), PL25298_3_V_F_E2.TPM (transcripts per million for sample PL25298 collected 3 days post-infection from a virus-infected female animal in experiment 2), PL25304_3_V_F_E2.TPM (transcripts per million for sample PL25304 collected 3 days post-infection from a virus-infected female animal in experiment 2), PL25161_6_V_M_E1.TPM (transcripts per million for sample PL25161 collected 6 days post-infection from a virus-infected male animal in experiment 1), PL25157_6_V_M_E1.TPM (transcripts per million for sample PL25157 collected 6 days post-infection from a virus-infected male animal in experiment 1), PL25158_6_V_F_E1.TPM (transcripts per million for sample PL25158 collected 6 days post-infection from a virus-infected female animal in experiment 1), PL25128_6_V_F_E1.TPM (transcripts per million for sample PL25128 collected 6 days post-infection from a virus-infected female animal in experiment 1), PL25136_6_V_M_E2.TPM (transcripts per million for sample PL25136 collected 6 days post-infection from a virus-infected male animal in experiment 2), PL25163_6_V_M_E2.TPM (transcripts per million for sample PL25163 collected 6 days post-infection from a virus-infected male animal in experiment 2), PL25228_6_V_F_E2.TPM (transcripts per million for sample PL25228 collected 6 days post-infection from a virus-infected female animal in experiment 2), PL25306_6_V_F_E2.TPM (transcripts per million for sample PL25306 collected 6 days post-infection from a virus-infected female animal in experiment 2), PL25124_3_C_M_E1.TPM (transcripts per million for sample PL25124 collected 3 days post-infection from a control male animal in experiment 1), PL25160_3_C_F_E1.TPM (transcripts per million for sample PL25160 collected 3 days post-infection from a control female animal in experiment 1), PL25169_3_C_M_E1.TPM (transcripts per million for sample PL25169 collected 3 days post-infection from a control male animal in experiment 1), PL25281_3_C_M_E2.TPM (transcripts per million for sample PL25281 collected 3 days post-infection from a control male animal in experiment 2), PL25152_3_C_M_E2.TPM (transcripts per million for sample PL25152 collected 3 days post-infection from a control male animal in experiment 2), PL25225_3_C_F_E2.TPM (transcripts per million for sample PL25225 collected 3 days post-infection from a control female animal in experiment 2), PL25226_3_C_F_E2.TPM (transcripts per million for sample PL25226 collected 3 days post-infection from a control female animal in experiment 2), PL25159_6_C_M_E1.TPM (transcripts per million for sample PL25159 collected 6 days post-infection from a control male animal in experiment 1), PL25018_6_C_F_E1.TPM (transcripts per million for sample PL25018 collected 6 days post-infection from a control female animal in experiment 1), PL25167_6_C_F_E1.TPM (transcripts per million for sample PL25167 collected 6 days post-infection from a control female animal in experiment 1), PL25280_6_C_M_E2.TPM (transcripts per million for sample PL25280 collected 6 days post-infection from a control male animal in experiment 2), PL25287_6_C_M_E2.TPM (transcripts per million for sample PL25287 collected 6 days post-infection from a control male animal in experiment 2), PL25313_6_C_F_E2.TPM (transcripts per million for sample PL25313 collected 6 days post-infection from a control female animal in experiment 2), PL25219_6_C_F_E2.TPM (transcripts per million for sample PL25219 collected 6 days post-infection from a control female animal in experiment 2).

4. Missing data codes: None

5. Specialized formats or other abbreviations used: None