General information

1. Title of Dataset: Transcriptome of Peromyscus leucopus 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: milovica@uci.edu

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 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: preprint
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: Manuscript in preparation; preprint server DOI pending

Data & file overview

1. File List: Lungs_TPM
2. Relationship between files, if important: Not applicable
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. The project and the description of the samples are described under the following NCBI BioProjects: PRJNA1026365 (https://www.ncbi.nlm.nih.gov/bioproject/[PRJNA1026365](https://dataview.ncbi.nlm.nih.gov/object/PRJNA1026365)). The experimental design for the first trial involves using adult male and female P. leucopus LL stock. Animals were dosed with nasal inhalation of either tissue culture medium (DMEM) alone (controls) or alpha variant, WA1 strain of SARS-CoV-2 virus. We dosed 8 animals with a virus (titer 2x10⁴) and 6 with DMEM alone. Animals were euthanized at either 3 or 6 days post-infection. For a second trial, P. leucopus animals were 1-3 years old and we had 3 groups: control animals with nasal inhalation of media, control animals with nasal inhalation of the heat-treated virus, and infected animals. Each group has 4 animals euthanized on 3- or 6-days post-infection (DPI). Lung tissue was used for RNA isolation and further sequencing to obtain 40 x 10⁶ PE150 reads.
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: Lungs_TPM.csv

1. Number of variables: 42
2. Number of cases/rows: 54467 rows (including header)
3. Variable List: transcript (NCBI species accession number), length (gene length), gene (gene name), product (long gene name), animalID.TPM (animal ID, starting with letters PL referring to species, TPM expressed in rows for each gene),
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None