Data for: High elevation adaptation is associated with functional changes in the immune response of deer mice
Data files
Mar 02, 2026 version files 85.56 MB
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accuracyData.csv
858 B
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bodyweightdata.csv
3.70 KB
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Cleaned_Temp_Data.csv
61.81 MB
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cort_analysis_revised.R
1.28 KB
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FC_BW_rev.R
5.68 KB
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foodconsumptiondata.csv
7.20 KB
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GeneratingResiduals_TbPlots.r
6.47 KB
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GOandGSEA_Rev.R
2.82 KB
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MergedDE_ortho_pManual.csv
5.21 MB
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mergedresid.csv
7.77 MB
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parallelismAndAccuracyTest.R
501 B
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ParallelismData.csv
797 B
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Pman_GCF_readcounts.xlsx
7.69 MB
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README.md
16.01 KB
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Rest_window_stats.R
1.16 KB
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Rest_Window.R
1.51 KB
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restwindow_8AM.csv
11.67 KB
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saline_mice_cleaned.csv
2.02 MB
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Seq_analysis_DREAM_rev.R
4.50 KB
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serumCORT.csv
2.40 KB
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spleen_metadata.xlsx
10.84 KB
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Tb_residual_stats.R
2.78 KB
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Tissues.R
4.52 KB
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TissueVals.csv
1.97 KB
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trialdate.csv
115 B
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V_sorted.csv
966.32 KB
Abstract
Adaptation to high altitude environments shapes whole organism physiology, but effects on the immune system are relatively understudied. These datasets, data processing scripts, and analyses evaluate whether local adaptation to high altitudes in the North American deer mouse (Peromsycus maniculatus) has led to differentiation in and differential function of the immune system. Deer mice derived from low and high altitude populations were bred in a common-garden environment and challenged with lipopolysaccharide (LPS), a component of bacterial cell walls. We collected data on the febrile response (fever) and acute phase response (body mass loss and anorexia) over 12 days following LPS challenge. We also collected data on phenotypic metrics and splenic tissue following an acute challenge with the same LPS dose. Together, these data and analyses demonstrate that low and high-altitude deer mice have diverged in their immune responses to a common challenge in ways that may be consequential for novel pathogen spread in high altitude environments.
Dataset DOI: 10.5061/dryad.gtht76j0p
Description of the data and file structure
Deer mice (Peromyscus maniculatus) derived from 2 populations (lowland and highland) were subjected to a bacterial immune challenge (LPS) to elicit an innate immune response. In these mice, we collected body temperatures via PIT-tags to assess the febrile response, tracked metabolic recovery (body weight change and food consumption), analyzed serum corticosterone, and examined differential expression of genes from RNA-seq of the spleen. The effects of LPS were compared to a saline control for these parameters.
Files and variables
File: Cleaned_Temp_Data.csv
Description: Temperature data collected from mice. This file has been cleaned using scripts posted previously.
Variables
- Trial: Round of experiments (1-4)
- Tag.ID: Unique PIT-Tag ID that the read corresponds to
- Date: Date of the read
- Time: Time of the read
- Antenna: Antenna from which the data were read
- Tag.Data
- Temp: Temperature read (degree C)
- Max: Maximum temperature read from this tag
- Pop.TRI: Marker column for time relative to injection per population (factor; KN_before, KN_after, ME_before, or ME_after)
- Population: Ancestry (KN or ME)
- Inj_Date: Date of injection
- Inj_Time: Time of injection
- DT: Date-time reformatted Date and Time columns (of read)
- Injection_Date: Date-time reformatted column of Inj_Date and Inj_Time
- Time Relative to Injection (Hours): Time relative to injection in hours
- Time Relative to Injection (pre or post): Categorical descriptor on time relative to injection (before or after)
File: bodyweightdata.csv
Description: Body weight data in long-form for analysis
Variables
- ID: Unique animal ID
- Day: Day of data collection (in experimental timeline)
- BW: Body mass (in grams)
- Population: Ancestry (KN [lowland] or ME [highland])
- BWL: Body mass (in grams) change from prior day
- BWC from D0: Body mass (in grams) change from day 0
File: trialdate.csv
Description: Records of injection date for the four trial cohorts
Variables
- Trial: Trial ID (1-4)
- Injection_Date: Date and time of injection (MM/DD/YYYY HH:MM:SS)
File: V_sorted.csv
Description: Processed temperature data with keep/discard labels per temperature measurement.
Variables
- Date: Date stamp of temperature data measurement (MM/DD/YY)
- Time: Time stamp of temperature data measurement (HH:MM:SS)
- Antenna: Antenna number from which the temperature was read
- Tag.ID: Unique PIT-tag id (unique individual)
- Tag.Data: Alternative unique marker
- Temp: Temperature reading from the PIT-Tag
- Max: Maximum temperature recorded by the tag
- DT: Date-Time column (created from Date and Time)
- keep: column with marks for keep or discard of erroneous reads
File: restwindow_8AM.csv
Description: Binned temperature data per individual for rest window analysis.
Variables
- ID: Unique mouse ID
- Day: Day relative to injection (-10 to 0)
- Mean Tb: Average body temperature calculated for the window
- Median Tb: Median body temperature calculated for this window
- Min Tb: Minimum body temperature calculated for this window
- Max Tb: Maximum body temperature calculated for this window
- Time: Window ID (all are 8 am-noon)
- Date: Date of measurement (Day-Mo)
- Trial: Trial round (1-3)
- Populations: Ancestry (KN or ME for lowland or highland, respectively)
File: saline_mice_cleaned.csv
Description: Temperature data collected from saline-only injected mice. This file has been cleaned using scripts posted previously.
Variables
- Tag.ID: Unique PIT-Tag ID that the read corresponds to
- Date: Date of the read
- Time: Time of the read
- Antenna: Antenna from which the data were read
- Tag.ID: Unique PIT-Tag ID value
- Tag.Data: Time since prior read
- Temp: Temperature read
- DT: Date-time reformat of Date and Time columns (for read)
- keep: column used in cleaning to indicate keep or remove
- Injection_Date: Date of saline injection
- TRI: Time relative to injection (in hours)
- time_category: Categorical descriptor on time relative to injection (before or after)
File: TissueVals.csv
Description: Tissue-level phenotypic data collected from mice at the termination of the experiments.
Variables
- Mouse ID: Unique mouse ID
- PIT TAG: Unique PIT-tag ID that is read bythe temperature device
- Family: Family group for each unique mouse
- Altitude: Ancestry (lowland or highland)
- Population: Shorthand for populations (KN, Kearney, Nebraska [lowland]; ME, Mount Evans [highland])
- Date_Coll: Date animal was sampled
- Inj #2: Type of injection before dissection (LPS or saline)
- BW start: Body weight at the start of the experiment
- BW end: Body weight at the time of sampling
- spleen weight (g): Weight of the spleen at dissection
File: foodconsumptiondata.csv
Description: Long-form food consumption data for analysis.
Variables
- ID: Unique animal ID
- Day: Day of data collection (in experimental timeline)
- BW: Body mass (in grams)
- Population: Ancestry (KN [lowland] or ME [highland])
- BWL: Body mass (in grams) change from prior day
- BWC from D0: Body mass (in grams) change from day 0
- D0.BW: Body mass (in grams) on day 0 of the experiment
- Food consump: food consumed in the prior 48-hour window (in grams)
- %BW: body mass on that experimental day expressed as a percent of D0 body mass
File: serumCORT.csv
Description: Baseline corticosterone values for each mouse were measured via ELISA.
Variables
- Date: Date that the assay was run
- Plate: Plate ID
- Pop: Ancestry of individual (KN [lowland] or ME [highland])
- Inj_2: Injection type prior to sample collection (SAL [saline] or LPS)
- Family: Family of animals from which the sample was collected
- Trial: Cohort in which the animal was run through the experimental paradigm
- Other: Order in which animal was sampled on the day of sampling (1 = first, with increasing numbers indicating individuals that were sampled later during the sampling period)
- SampleID: unique animal ID
- DilutionFactor: The factor by which the serum was diluted for assay
- Avg_conc: Concentration of corticosterone read from the plate, averaged across 3 replicates (pg/mL)
- avg_conc*DF: Avg_conc multiplied by the DilutionFactor (pg/mL)
- ngpermL_CORRECTED: avg_conc*DF converted to ng/mL
- dilution round: Round in which the sample was initially extracted
File: ParallelismData.csv
Description: Data used for the validation test of parallelism for CORT ELISA.
Variables
- Label: Sample ID
- curve: Curve (std [Standard] or samp [test sample])
- rep1: absorbance value from replicate well 1
- rep2: absorbance value from replicate well 2
- avg abs: average absorbance across the two wells
- exp conc: expected concentration of corticosterone (pg/mL) assuming a two-fold dilution series across the samples.
- logconc: log() of the expected concentration
File: mergedresid.csv
Description: File of residual body temperature values for individuals across the experimental period.
Variables
- ID: Unique PIT-tag ID per mouse
- Pop: Ancestry (KB or ME, referring to the lowland or highland populations respectively)
- actual: Raw temperature value
- difference: the residual or difference between the raw temperature value (actual) and the expected temperature values based on individually-modeled temperature curves.
- TRI: Time relative to injection, expressed as a decimal for use in the calculation of the expected temperature and difference.
File: spleen_metadata.xlsx
Description: Metadata for transcriptomic analysis from spleens
Variables
- Mouse_ID: Unique mouse ID (different from PIT-Tag IDs)
- RNA_Name: RNA sequence file ID
- Pop: Ancestry (KN or ME, referring to lowland or highland populations respectively)
- Family: Family ID for each mouse, referencing the breeding pair from which each individual was generated
- Inj_2: Type of injection received prior to spleen collection (SAL or LPS)
- Trial: Trail ID for mouse cohorts
- Group: A dummy variable for group using the format [Trial][Pop][Inj_2]
- Seq_Name: Full name of the sequence file containing transcriptomic read information and aligning with the output from featureCounts (Pman_GCF_readcounts.xlsx)
File: Pman_GCF_readcounts.xlsx
Description: Read counts for genes as compiled by featureCounts from raw RNAseq files from spleens.
Variables
- Geneid: Gene name (Pman)
- Chr: Chromosome location of gene
- Start: Start location of gene within chromosome (Chr)
- End: End location of gene within chromosome (Chr)
- Strand: strand on which the gene is located (+ or -)
- Length: Gene length in bp
- Sp[...].bam (Columns 7-40 or G-AM): column names using this general nomenclature contain read counts per sample, where the column name is the sample ID. These sample IDs can be matched to individual IDs in the spleen_metadata.xlsx file.
File: parallelismAndAccuracyTest.R
Description: Script for plots and analysis related to the validation of the CORT ELISA
File: cort_analysis_revised.R
Description: Script for statistical evaluation of differences in experimental CORT samples between populations (low or high) and injection types (LPS or SAL).
File: Tissues.R
Description: Script for statistical evaluation of differences in phenotypic data (tissuevals.csv) between populations (low or high) and injection types (LPS or SAL).
File: accuracyData.csv
Description: Data used for the validation test of accuracy for CORT ELISA.
Variables
- sampleID: Sample ID
- poolwStd_quant: Measured concentration of CORT in the sample well (pg/mL)
- poolwStd_expected: Expected concentration of CORT in the sample well (pg/mL) (pool_Neat + known concentration of standard)
- pctDiff: percent difference between the measured and expected values.
File: Rest_window_stats.R
Description: Script to test for population differences in rest-phase body temperatures across animals.
File: Rest_Window.R
Description: Script to extract min, max, mean, and median temp values for the rest phase on a per-animal basis.
File: Tb_residual_stats.R
Description: Script to test for population differences in residual body temperature (LPS vs baseline) across the experimental time period for all animals.
File: FC_BW_rev.R
Description: Script for statistically evaluating population-level differences and LPS-related changes in food consumption.
File: Seq_analysis_DREAM_rev.R
Description: Script for read filtering, normalization, and differential expression analysis.
File: GeneratingResiduals_TbPlots.r
Description: Script for generating residual values from individual body temperature datasets. This script was run for each individual (i.e., per unique PIT-Tag ID). Data for each individual (from Cleaned_Temp_Data.csv) was separated into pre- and post-injection using trialdate.csv to generate PRE_A.csv (pre-injection) and POST_A.csv (post-injection) temperature data prior to running this script per individual. The residual output from this script (line 46, prA_ds$residuals) was then merged for all individuals and can be found in the file mergedresid.csv.
File: GOandGSEA_Rev.R
Description: Script to reproduce GO and GSEA analyses.
File: MergedDE_ortho_pManual.csv
Description: Summary file of differential expression output also used for GO and GSEA input.
Variables
- : Line numbers
- X: Line numbers
- rowname: Gene name (P maniculatus)
- initial_ensg: Ensembl ID (P maniculatus)
- ortholog_name: Mus gene name (M musculus)
- ortholog_ensg: Ensembl ID (M musculus)
- description: Gene description (M musculus)
- ComparativeList_mus: Y/N (1/0) dummy variable to identify genes that were differentially expressed in response to LPS in M musculus spleen from Balderrama-Gutierrez et al. 2021.
- ComparativeList_pleu: Y/N (1/0) dummy variable to identify genes that were differentially expressed in response to LPS in P leucopus spleen from Balderrama-Gutierrez et al. 2021.
- X1: Y/N (1/0) dummy variable to identify genes that were differentially expressed in response to LPS in either M musculus or P leucopus spleen from Balderrama-Gutierrez et al. 2021.
- Schweizer: Y/N (1/0) dummy variable to identify genes that were identified as targets of selection in Schweizer et al 2019.
- logFC.Pop: log-fold change in gene expression by population (from dream analysis)
- AveExpr.Pop: average expression of a gene by a population (from dream analysis)
- t.Pop: t-statistic for the effect of population (from dream analysis)
- P.Value.Pop: raw p-value for the effect of population (from dream analysis)
- adj.P.Val.Pop: adjusted p-value for the effect of population (from dream analysis)
- B.Pop: effect size of population (from dream analysis)
- logFC.Inj: log-fold change in gene expression by injection type (from dream analysis)
- AveExpr.Inj: average expression of gene by injection type (from dream analysis)
- t.Inj: t-statistic for the effect of injection type (from dream analysis)
- P.Value.Inj: raw p-value for the effect of injection type (from dream analysis)
- adj.P.Val.Inj: adjusted p-value for the effect of injection type (from dream analysis)
- B.Inj: effect size of injection type (from dream analysis)
- logFC.PopByInj: log-fold change in gene expression for the interaction between population and injection type (from dream analysis)
- AveExpr.PopByInj: average expression for the interaction between population and injection type (from dream analysis)
- t.PopByInj: t-statistic of the interaction between population and injection type (from dream analysis)
- P.Value.PopByInj: raw p-value for the effect of an interaction between population and injection type (from dream analysis)
- adj.P.Val.PopByInj: adjusted p-value for the effect of an interaction between population and injection type (from dream analysis)
- B.PopByInj: effect size of an interaction between population and injection type (from dream analysis)
- PopSig: Y/N (1/0) dummy variable to identify genes that were differentially expressed between populations at FDR < 0.05
- InjSig: Y/N (1/0) dummy variable to identify genes that were differentially expressed by injection type at FDR < 0.05
- AddSig: Y/N (1/0) dummy variable to identify genes that were differentially expressed both between populations and by injection type at FDR < 0.05
- PopManualPvalAdj: adjusted p-value for the effect of an interaction between populations (manual adjustment, see main text)
- InjManualPvalAdj: adjusted p-value for the effect of injection type (manual adjustment, see main text)
- IxnManualPvalAdj: adjusted p-value for the effect of an interaction between population and injection type (manual adjustment, see main text)
- Add: Y/N (1/0) dummy variable to identify genes that were differentially expressed both between populations and by injection type at FDR < 0.05 among manually-adjusted p-values
- sum: Count of categories fulfilled for this gene
- PopGSEA: -log10(raw p-values)*logFC for the effect of population for ranking in GSEA
- InjGSEA: -log10(raw pvalues)*logFC for the effect of injection type for ranking in GSEA
- IxnGSEA: -log10(raw pvalues)*logFC for the interaction between injection type and population for ranking in GSEA
Code/software
All data were handled and processed in R. Scripts are described above.
Access information
Other publicly accessible locations of the data:
- Raw sequence data are available from BioProject PRJNA1250593 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1250593)
