Data from: Peromysus leucopus and Mus musculus transcriptomic analysis of lungs infected with Sars-CoV-2
Data files
Mar 25, 2026 version files 13.66 MB
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Mus_Peromyscus.xlsx
13.65 MB
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README.md
11.02 KB
Abstract
This dataset comprises RNA sequencing (RNA-seq) data from lung tissues of Peromyscus leucopus and K18-hACE2Mus musculus infected with SARS-CoV-2, and controls. The study aimed to analyze the transcriptional landscape and identify and compare differentially expressed genes in this critical organ upon viral infection between two rodent species. Tissue samples were collected from infected subjects on day 3 and day 6 post-infection in P. leucopus and days 2, 4 and 7 in M. musculus. Total RNA was extracted, and RNA-seq libraries were prepared and sequenced using high-throughput sequencing platforms. The resulting raw sequencing reads were processed and aligned to the reference set of P. leucopus and M. musculus coding DNA sequence (CDS). Gene expression levels were quantified and normalized by average gene reads and housekeeping gene Glyceraldehyde 3-phosphate dehydrogenase (Gapdh) and expressed as natural logarithm of the value.
GENERAL INFORMATION
1. Peromysus leucopus and Mus musculus transcriptomic analysis of 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 and https://doi.org/10.1038/s41590-020-0778-2
3. Links to other publicly accessible locations of the data: https://doi.org/10.1038/s41590-020-0778-2
4. Links/relationships to ancillary data sets: See below for BioProject numbers.
5. Was data derived from another source? yes
A. If yes, list source(s): https://doi.org/10.1038/s41590-020-0778-2
6. Recommended citation for this dataset: Manuscript in preparation; preprint server DOI pending
DATA & FILE OVERVIEW
1. File List: Mus_Peromyscus.xlsx
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
DATA-SPECIFIC INFORMATION FOR: Mus_lungs_GAPDH
1. Number of variables: 21
2. Number of cases/rows: 22762 rows (including header)
3. Variable List:
Gene_name (gene symbol or identifier corresponding to each row in the gene expression matrix), Mus_Naive_Lung_F_SRR12185412 (transcripts per million for a female naive mouse lung sample, SRA accession SRR12185412),
Mus_Naive_Lung_F_SRR12185413 (transcripts per million for a female naive mouse lung sample, SRA accession SRR12185413),
Mus_Naive_Lung_F_SRR12185414 (transcripts per million for a female naive mouse lung sample, SRA accession SRR12185414),
Mus_Naive_Lung_F_SRR12185415 (transcripts per million for a female naive mouse lung sample, SRA accession SRR12185415),
Mus_Sars_Lung_F_DPI2_SRR12185416 (transcripts per million for a female mouse lung sample 2 days post SARS infection, SRA accession SRR12185416),
Mus_Sars_Lung_F_DPI2_SRR12185417 (transcripts per million for a female mouse lung sample 2 days post SARS infection, SRA accession SRR12185417),
Mus_Sars_Lung_F_DPI2_SRR12185418 (transcripts per million for a female mouse lung sample 2 days post SARS infection, SRA accession SRR12185418),
Mus_Sars_Lung_M_DPI2_SRR12185419 (transcripts per million for a male mouse lung sample 2 days post SARS infection, SRA accession SRR12185419),
Mus_Sars_Lung_F_DPI2_SRR12185420 (transcripts per million for a female mouse lung sample 2 days post SARS infection, SRA accession SRR12185420),
Mus_Sars_Lung_M_DPI4_SRR12185421 (transcripts per million for a male mouse lung sample 4 days post SARS infection, SRA accession SRR12185421),
Mus_Sars_Lung_M_DPI4_SRR12185422 (transcripts per million for a male mouse lung sample 4 days post SARS infection, SRA accession SRR12185422),
Mus_Sars_Lung_M_DPI4_SRR12185423 (transcripts per million for a male mouse lung sample 4 days post SARS infection, SRA accession SRR12185423),
Mus_Sars_Lung_F_DPI4_SRR12185424 (transcripts per million for a female mouse lung sample 4 days post SARS infection, SRA accession SRR12185424),
Mus_Sars_Lung_F_DPI4_SRR12185425 (transcripts per million for a female mouse lung sample 4 days post SARS infection, SRA accession SRR12185425),
Mus_Sars_Lung_F_DPI4_SRR12185426 (transcripts per million for a female mouse lung sample 4 days post SARS infection, SRA accession SRR12185426),
Mus_Sars_Lung_M_DPI7_SRR12185427 (transcripts per million for a male mouse lung sample 7 days post SARS infection, SRA accession SRR12185427),
Mus_Sars_Lung_M_DPI7_SRR12185428 (transcripts per million for a male mouse lung sample 7 days post SARS infection, SRA accession SRR12185428),
Mus_Sars_Lung_F_DPI7_SRR12185429 (transcripts per million for a female mouse lung sample 7 days post SARS infection, SRA accession SRR12185429),
Mus_Sars_Lung_F_DPI7_SRR12185430 (transcripts per million for a female mouse lung sample 7 days post SARS infection, SRA accession SRR12185430),
Mus_Sars_Lung_M_DPI7_SRR12185431 (transcripts per million for a male mouse lung sample 7 days post SARS infection, SRA accession SRR12185431).
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None
DATA-SPECIFIC INFORMATION FOR: Peromyscus_lungs_GAPDH
1. Number of variables: 31
2. Number of cases/rows: 22668 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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25124 collected 3 days post-treatment from a control male animal in experiment 1),
PL25160_3_C_F_E1 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25160 collected 3 days post-treatment from a control female animal in experiment 1),
PL25169_3_C_M_E1 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25169 collected 3 days post-treatment from a control male animal in experiment 1),
PL25281_3_C_M_E2 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25281 collected 3 days post-treatment from a control male animal in experiment 2),
PL25152_3_C_M_E2 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25152 collected 3 days post-treatment from a control male animal in experiment 2),
PL25225_3_C_F_E2 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25225 collected 3 days post-treatment from a control female animal in experiment 2),
PL25226_3_C_F_E2 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25226 collected 3 days post-treatment from a control female animal in experiment 2),
PL25159_6_C_M_E1 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25159 collected 6 days post-treatment from a control male animal in experiment 1),
PL25018_6_C_F_E1 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25018 collected 6 days post-treatment from a control female animal in experiment 1),
PL25167_6_C_F_E1 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25167 collected 6 days post-treatment from a control female animal in experiment 1),
PL25280_6_C_M_E2 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25280 collected 6 days post-treatment from a control male animal in experiment 2),
PL25287_6_C_M_E2 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25287 collected 6 days post-treatment from a control male animal in experiment 2), PL25313_6_C_F_E2 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25313 collected 6 days post-treatment from a control female animal in experiment 2),
PL25219_6_C_F_E2 (number of uniquely mapped RNA-seq reads assigned to each gene for sample PL25219 collected 6 days post-treatment from a control female animal in experiment 2).
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None
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. 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 animals with a either a virus (titer 2x104) and 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 the same design. Lung tissue was used for RNA isolation and further sequencing to obtain reads. Mus musculus were also inoculated with 2.5x104 of the same virus and lung tissue was collected on days 2, 4 and 7. Transcripts were mapped to respective genomes and normalized to average gene reads and housekeeping gene Gapdh. Data for each animal is expressed zs natural logarithm of the normalized value.
2. Instrument- or software-specific information needed to interpret the data: NA
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