DOI: 10.5061/dryad.37pvmcvrx
title: Transcriptome of Peromyscus leucopus lungs infected with SARS-CoV-2

description: 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. 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.
description: Lung RNA was isolated using Direct-zol Miniprep kit according to
 instructions. Lung RNA was sequenced using Illumina technology. The
 stranded mRNA library was normalized, multiplexed, and sequences on the
 NovaSeq6000 instrument at the UC Irvine genomic High Throughput Facility.
 We used paired-end chemistry and 150 cycles to achieve 40 million reads
 per sample.  The project and the description
 of the samples are described under the following NCBI BioProjects: PRJNA1026365 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1026365). Manuscript in preparation; URL pending.
description: GENERAL INFORMATION 1. Title of Dataset: Transcriptome of Peromyscus
 leucopus lungs infected with SARS-CoV-2 2. Author Information A. Principal
 Investigator Contact Information <br> Name: Alan G. Barbour
 <br> Institution: University of California Irvine <br>
 Address: 843 Health Sciences Court, Irvine, CA 92697 <br> Email:
 abarbour@uci.edu <br> B. Associate or Co-investigator Contact
 Information <br> Name: Ana Milovic <br> Institution:
 University of California Irvine <br> Address: 843 Health Sciences
 Court, Irvine, CA 92697 <br> 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: 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: 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. Since they live near humans we are interested in
 the possibility of SARS-CoV-2 infection in this animal model from a
 zoonoses standpoint. The project and the description of the samples are
 described under the following NCBI BioProjects:
 [PRJNA1026365](https://dataview.ncbi.nlm.nih.gov/object/PRJNA1026365) (https://www.ncbi.nlm.nih.gov/bioproject/[PRJNA1026365](https://dataview.ncbi.nlm.nih.gov/object/PRJNA1026365)). Manuscript in preparation; URL pending. 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 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