Dermal fibroblast cultures recapitulate differences between deermice and mice in responses to a Toll-like receptor agonist
Data files
Nov 04, 2025 version files 176.63 MB
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README.md
5.34 KB
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Table_D7.xlsx
2.09 MB
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Table_D8.xlsx
28.81 MB
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Table_D9.xlsx
35.31 MB
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TableD1_Peromyscus_CDS_22K.xlsx
5.39 MB
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TableD2_Mus_CDS_22K.xlsx
5.31 MB
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TableD3_PM_paired_14K.xlsx
2.28 MB
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TableD4_Peromyscus_ERV_1M.xlsx
46.81 MB
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TableD5_Mus_ERV__1M.xlsx
38.21 MB
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TableD6_PM_ERV_100k_FC.xlsx
12.42 MB
Abstract
The white-footed deermouse Peromyscus leucopus is a primary reservoir for the agents of Lyme disease and other zoonoses in North America. These and other species of Peromyscus are tolerant of the infection by the bacteria, protozoa, and viruses they host. This is mainly achieved by mitigating the damaging effects of the innate immune response. In previous studies, we demonstrated differences between P. leucopus and either inbred or outbred M. musculus in the degree of sickness and profiles of biomarkers after exposure to bacterial lipopolysaccharide, a TLR4 agonist. To develop a method for broadly assessing of innate immunity of capture-release mammals in nature, we evaluated using bulk and single-cell RNA-seq primary dermal fibroblast cultures of P. leucopus and M. musculus in their short-term responses to a lipopeptide that is a TLR2 agonist. As we had observed for experimental animals, the fibroblast cultures of the two species displayed both similarities and differences in their responses to the agonist. The notable differences included the greater magnitude of an anti-viral profile of cytokines and other effectors in the deermouse fibroblasts and the occurrence of an interleukin-11 response in the mouse cultures but not deermouse. We also observed in both species' cultures an increased transcription of several types of endogenous retrovirus (ERV) elements after exposure of the cells to the agonist. The P. leucopus cells were distinguished from M. musculus cells in the generally shorter retroviral open reading frames among the differentially expressed sequences. This was consistent with previous findings about ERV transcription in P. leucopus and M. musculus and suggests a greater suppression of ERV activity in P. leucopus. The results affirm the feasibility of this in vitro model for both laboratory- and field-based studies without need for euthanasia, and that inherent differences between deermice and mice in innate immune responses can be demonstrated in primary fibroblasts as well as the animals themselves.
Dataset DOI: 10.5061/dryad.m905qfvdq
Description of the data and file structure
Peromyscus leucopus and Mus musculus RNA-seq data of coding sequences (CDS), endogenous retroviruses (ERVs) and species comparisons across treatment groups of control or 1 µg/ml or 10 µg/ml Pam3CSK4.
Files and variables
File: TableD6_PM_ERV_100k_FC.xlsx
Description: Table D6. ERV/TEs ≥500 bp of P. leucopus and M. musculus dermal fibroblasts without (control) or with 1 µg/ml Pam3CSK4 and by length, transcription, and fold change of treatment to control.
Column names: ERV ≥500, genome location, length (bp), mean transcription control, mean transcription 1 µg/ml Pam3CSK4, log2 fold chain (FC).
File: TableD1_Peromyscus_CDS_22K.xlsx
Description: Table D1. Peromyscus leucopus dermal fibroblast normalized RNA-seq reads per kb of genome-wide CDS by animal source, treatment (control or 1 µg/ml or 10 µg/ml Pam3CSK4), and comparison of 1 µg/ml treatment to control by paired t-test and mean paired fold-change, and mean transcription across all samples by gene
Column names: gene, length in base pairs (bp), 25417 control, 25418 control, 25459 control, 25510 control, 25558 control, 25417 1µg/ml, 25418 1µg/ml, 25459 1µg/ml, 25510 1µg/ml, 25558 1µg/ml, 25417 10µg/ml, 25418 10µg/ml, 25459 10µg/ml, 25510 10µg/ml, 25558 10µg/ml, paired t-test 1 µg/ml vs control, fold-change 1 µg/ml vs control, log10 mean transcription (n=15)
File: TableD4_Peromyscus_ERV_1M.xlsx
Description: Table D4. Endogenous retrovirus (ERV) /transposable element sequences by name, genome location, and length of Peromyscus leucopus LL stock
Column names: ERV name, location, length in base pairs (bp).
File: TableD5_Mus_ERV__1M.xlsx
Description: Table D5. Endogenous retrovirus/transposable element sequences by name, genome location, and length of Mus musculus C57BL/6.
Column names: ERV name, location, length in base pairs (bp).
File: TableD2_Mus_CDS_22K.xlsx
Description: Table D2. Mus musculus dermal fibroblast normalized RNA-seq reads per kb of genome-wide CDS by animal source, treatment (control or 1 µg/ml or 10 µg/ml Pam3CSK4), and comparison of 1 µg/ml treatment to control by paired t-test and mean paired fold-change, and mean transcription across all samples by gene.
Column names: gene, length in base pairs (bp), MF1 control, MF2 control, MF3 control, MM1 control, MM2 control, MF1 1 µg/ml, MF2 1 µg/ml, MF3 1 µg/ml, MM1 1 µg/ml, MM2 1 µg/ml, MF1 10 µg/ml, MM2 10 µg/ml, MF3 10 µg/ml, MM1 10 µg/ml, MF2 10 µg/ml, paired t-test 1 µg/ml vs control, fold-change 1 µg/ml vs control, log10 mean transcription (n=15)
File: TableD3_PM_paired_14K.xlsx
Description: Table D3.Paired treatment-to-control fold-change (FC) and paired t-tests of transcribed (TPM≥10) CDS (n= 14,979) in common for M. musculus (M) and P. leucopus (P) treated with Pam3CSK4 at 1 µg (01) or 10 µg/ml (10).
Column names: gene, log2 FC M01, ttest p M01, log2 FC M10, ttest p M10, log2 FC P01, ttest p P01, log2 FC P10, ttest p P10, P01/M01 FC
File: Table_D7.xlsx
Description: Differential gene expression of dermal fibroblasts to TLR agonist by isoform for 13,786 genes of Mus musculus for which there are two isoforms for protein coding sequences
Column names: gene name first_isoform, length_1 (bp), TPM mean 1, fold change (FC) 1, log₂ FC 1, FDR p-value 1, gene name second_isoform, length_2 (bp), TPM mean 2, fold change (FC) 2, log₂ FC 2, FDR p-value 2
File: Table_D8.xlsx
Description: Differential experssion of ERV/TEs ≥500 bp of Mus musculus (Table D5) in low-passage dermal fibroblasts untreated or treated with 1 µg/ml Pam3CSK4
Column names: M. musculus ERV/TE, genome location, sequence length, log10 length, z_score length, MF2 1 µg/ml TPM, MF3 1 µg/ml TPM, MM2 1 µg/ml TPM, MM1 1 µg/ml TPM, MF1 1 µg/ml TPM, MF2 cont TPM, MF3 cont TPM, MM2 cont TPM, MM1 cont TPM, MF1 cont TPM, mean TPM, log10 MF2_1, log10 MF3_1, log10 MM2_1, log10 MM1_1, log10 MF1_1, log10 MF2_C, log10 MF3_C, log10 MM2_C, log10 MM1_C, log10 MF1_C, paired t-test p, negative log10 p, fold change MF2, fold change MF3, fold change MM2, fold change MM1, fold change MF1, mean fold change, log2 mean fold change
File: Table_D9.xlsx
Description: Differential experssion of ERV/TEs ≥500 bp of Peromyscus leucopus (Table D4) in low-passage dermal fibroblasts untreated or treated with 1 µg/ml Pam3CSK4
Column names: P. leucopus ERV/TE, genome location, sequence length, log10 length, z_score length, 25558M 1 µg/ml, 25417F 1 µg/ml, 25459F 1 µg/ml, 25510M 1 µg/ml, 25418F 1 µg/ml, 25558M cont, 25417F cont, 25459F cont, 25510M cont, 25418F cont, mean TPM, log10 25558M_1, log10 25417F_1, log10 25459F_1, log10 25510M_1, log10 25418F_1, log10 25558M_C, log10 25417F_C, log10 25459F_C, log10 25510M_C, log10 25418F_C, paired t-test p, negative log10 p, fold change 25558M, fold change 25417F, fold change 25459F, fold change 25510M, fold change 25418F, mean fold change, log2 mean fold change
Code/software
Microsoft Excel can be used to view the files