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Data and code for the manuscript: "Transcriptional changes capture sex differences in vascularization in a skin coloration signal in a wild primate." Submission to Molecular Ecology.

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DeLacey_et_al_chest_skin_transcription_2023.R

DeLacey_et_al_chest_skin_transcription_2023.R

 
 

README.md

README.md

 
 

biopsies_AR.csv

biopsies_AR.csv

 
 

biopsies_ESR1.csv

biopsies_ESR1.csv

 
 

biopsies_ESR2.csv

biopsies_ESR2.csv

 
 

biopsies_PID_10120_mmul10.RData

biopsies_PID_10120_mmul10.RData

 
 

biopsies_genes.csv

biopsies_genes.csv

 
 

biopsies_hb_rrna_genes.csv

biopsies_hb_rrna_genes.csv

 
 

biopsies_meta_teeth.csv

biopsies_meta_teeth.csv

 
 

biopsies_metadata.csv

biopsies_metadata.csv

 
 

biopsies_mmul10_gene_chr.csv

biopsies_mmul10_gene_chr.csv

 
 

biopsies_red_anes_rna.csv

biopsies_red_anes_rna.csv

 
 

photo_red_anes.csv

photo_red_anes.csv

 
 

photo_red_heat_change_anes.csv

photo_red_heat_change_anes.csv

 
 

photo_red_nat.csv

photo_red_nat.csv

 
 

photo_red_range_nat.csv

photo_red_range_nat.csv

 
 

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README_Dataset-GeladaChestSkinTranscription_v0.1.0

Provenance for this README

  • File name: Dataset-GeladaChestSkinTranscription_v0.1.0.txt
  • Authors: Patricia M. DeLacey
  • Other contributors: Sharmi Sen, India A. Schneider-Crease, Kenneth L. Chiou, Alemayehu Lemma, Ferehiwot Ayele, Abebaw Haile, Amy Lu, Thore J. Bergman, Jacinta C. Beehner, Noah Snyder-Mackler
  • Date created: 2023-05-18
  • Date modified: 2023-05-21

Dataset Version and Release History

  • Current Version:

    • Number: 1.0.0
    • Date: 2023-05-21
    • Persistent identifier: DOI: 10.5061/dryad.sqv9s4n7p
    • Summary of changes: n/a

  • Embargo Provenance: n/a

    • Scope of embargo: n/a
    • Embargo period: n/a

Dataset Attribution and Usage

  • Dataset Title: Data from: Vascularization underlies differences in sexually selected skin coloration in a wild primate

  • Persistent Identifier: https://doi.org/10.5061/dryad.sqv9s4n7p

  • Dataset Contributors:

    • Creators: Patricia M. DeLacey, Sharmi Sen, India A. Schneider-Crease, Kenneth L. Chiou, Alemayehu Lemma, Ferehiwot Ayele, Abebaw Haile, Amy Lu, Thore J. Bergman, Jacinta C. Beehner, Noah Snyder-Mackler

  • Date of Issue: 2023-05-19

  • Publisher: University of Michigan

  • Suggested Citations:

    • Dataset citation:

      DeLacey, P.M., Sen, S., Schneider-Crease, I.A., Chiou, K.L., Lemma, A., Ayele, F., Haile, A.A., Lu, A., Bergman, T.J., Beehner, J.C., Snyder-Mackler, N. Data from: Vascularization underlies differences in sexually selected skin coloration in a wild primate, Dryad, Dataset, https://doi.org/10.5061/dryad.sqv9s4n7p

    • Corresponding publication:

      DeLacey, P.M., Sen, S., Schneider-Crease, I.A., Chiou, K.L., Lemma, A., Ayele, F., Haile, A.A., Lu, A., Bergman, T.J., Beehner, J.C., Snyder-Mackler, N. Vascularization underlies differences in sexually selected skin coloration in a wild primate. Molecular Ecology. Accepted. DOI: 10.22541/au.167359516.63326414/v1

Contact Information

Additional Dataset Metadata

Acknowledgements

  • Funding sources: This work was supported by the National Science Foundation (BCS-2041542, BCS-0715179, BCS-1732231, BCS-1723237, BCS-2010309, BCS-1723228, IOS-1255974, IOS-1854359), the Leakey Foundation (AWD015438), the Leakey Foundation Baldwin Award (AWD012312), the National Geographic Society (NGS-8100–06, NGS-8989–11, NGS-1242, and NGS-50409R-18), the Fulbright Scholars Program, Nacey Maggioncalda Foundation, Sigma Xi, the University of Michigan, Arizona State University, University of Washington, and Stony Brook University.

Dates and Locations

  • Dates of data collection: Field data collected between 2006 and 2020

  • Geographic locations of data collection: Fieldwork conducted in the Simien Mountains National Park, Ethiopia with the permission of the Ethiopian Wildlife Conservation Authority (see publication for more details)

  • Other locations pertaining to dataset contents: Wet lab work and sample sequencing performed at the University of Washington. Photo analyses conducted at the University of Michigan.

Methodological Information

  • Methods of data collection/generation: see manuscript for details

Data and File Overview

Summary Metrics

  • File count: 15
  • Total file size: 5.5 MB
  • Range of individual file sizes: 144 bytes - 3.55 MB
  • File formats: .csv, .RData, .R

Naming Conventions

  • File naming scheme: files with the "photo" prefix denote files that accompany the "Chest redness in male and female geladas" results subsection; files with the prefix "biopsies" denote files that accompany the "Sex differences in gene expression" and "Sex-biased genes involved in vascularization" results subsections.

Table of Contents

  • DeLacey_et_al_chest_skin_transcription_2023.R
  • photo_red_nat.csv
  • photo_red_range_nat.csv
  • photo_red_anes.csv
  • photo_red_heat_change_anes.csv
  • biopsies_PID_10120_mmul10.RData
  • biopsies_hb_rrna_genes.csv
  • biopsies_genes.csv
  • biopsies_metadata.csv
  • biopsies_meta_teeth.csv
  • biopsies_mmul10_gene_chr.csv
  • biopsies_AR.csv
  • biopsies_ESR1.csv
  • biopsies_ESR2.csv biopsies_red_anes_rna.csv

Setup

  • Unpacking instructions: n/a

  • Relationships between files/folders: The .R file contains a script that uses all the following .csv files to run analyses and generate graphs.

  • Recommended software/tools: RStudio 2023.03.0+386; R version 4.2.1

File/Folder Details

Details for: photo_red_nat.csv

  • Description: a comma-delimited file containing the male and female chest redness under natural conditions - not anesthetized

  • Format(s): .csv

  • Size(s): 4.44 KB

  • Dimensions: 144 rows x 5 columns

  • Variables:

    • id: three letter code for the individual gelada
    • rg: chest redness value (numerical ratio of red to green; see Methods)
    • camera_brand: brand of the digital camera used to take the photo (Nikon or Sony)
    • model: camera model used to take the photo
    • sex: genetic sex; F = female; M = male

Details for: photo_red_range_nat.csv

  • Description: a comma-delimited file containing male and female range in chest redness (max - min for each individual) under natural conditions - not anesthetized

  • Format(s): .csv

  • Size(s): 1.84 KB

  • Dimensions: 36 rows x 7 columns

  • Variables:

    • id:three letter code for the individual gelada
    • max: the maximum chest redness value (numerical ratio of red to green; see Methods) for this individual
    • min: the minimum chest redness value (numerical ratio of red to green; see Methods) for this individual
    • range: the maximum minus the minimum chest redness value for this individual
    • sex: genetic sex; F = female; M = male
    • N: number of samples per individual
    • camera_brand: brand of the digital camera used to take the photo (Nikon, Sony, or both)

Details for: photo_red_anes.csv

  • Description: a comma-delimited file containing male and female chest redness while anesthetized

  • Format(s): .csv

  • Size(s): 2.65 KB

  • Dimensions: 38 rows x 10 columns

  • Variables:

    • date: date the photo collected yy-mm-dd
    • collection_year: year the photo was collected
    • dart_id: capture-and-release program identification number for the individual in the format of year_three number code
    • id: three letter code for the individual gelada
    • rna_seq: if a skin biopsy was also collected for this individual, this includes the reference ID for that chest skin biopsy
    • sex: genetic sex; F = female; M = male
    • age_cat_teeth: adulthood was determined using the eruption of the third molar; categories include: adult male, adult female, subadult male, subadult female
    • mass_kg: mass in kilograms of the gelada
    • camera_brand: brand of the digital camera used to take the photo (Nikon or Sony)
    • rg: chest redness value (numerical ratio of red to green; see Methods)

Details for: photo_red_heat_change_anes.csv

  • Description: a comma-delimited file containing the change in redness between baseline and application of a heat pack directly to the skin compared between males and females

  • Format(s): .csv

  • Size(s): 764 bytes

  • Dimensions: 16 rows x 5 columns

  • Variables:

    • dart_id:capture-and-release program identification number for the individual in the format of year_three number code
    • sex: genetic sex; F = female; M = male
    • heat: chest redness value (numerical ratio of red to green) after application of a heat pack for one minute (see Methods)
    • none: chest redness value (numerical ratio of red to green) at baseline temperature
    • change: the difference between heat and none to get the change in chest redness

Details for: biopsies_PID_10120_mmul10.RData

  • Description: a .RData file containing a large matrix of gene counts mapped to the annotated Macaca mulatta genome

  • Format(s): .RData

  • Size(s): 3.55 MB

  • Dimensions: 22515 rows x 38 columns

  • Variables:

    • row names: ensembl gene name in the Macaque mulatta genome (Mmul_10)
    • columns 1-38: Library Identification Number (LID) for each of the 38 chest skin biopsies

Details for: biopsies_hb_rrna_genes.csv

  • Description: a comma-delimited file containing a list of hemoglobin and ribosomal RNA genes from the annotated macaca mulatta genome

  • Format(s): .csv

  • Size(s): 144 bytes

  • Dimensions: 8 rows x 1 columns

  • Variable:

    • gene: ensembl gene name in the Macaque mulatta genome (Mmul_10)

Details for: biopsies_genes.csv

  • Description: a comma-delimited file containing gene names for ensembl(V1) and VGNC(V2)

  • Format(s): .csv

  • Size(s): 999.95 KB

  • Dimensions: 32386 rows x 2 columns

  • Variables:

    • V1: Ensembl gene name
    • V2: Vertebrate Gene Nomenclature Committee (VGNC) gene name

Details for: biopsies_metadata.csv

  • Description: a comma-delimited file containing the technical and biological variables from all skin biopsy samples

  • Format(s): .csv

  • Size(s): 2.18 KB

  • Dimensions: 38 rows x 9 columns

  • Variables:

    • LID: Library Identification Number for chest skin biopsy samples
    • ID: capture-and-release program identification number for the individual in the format of year_three number code
    • Year: Year the skin biopsy sample was collected during the capture-and-release campaigns
    • Sex: genetic sex; F = female; M = male
    • RID_date: date the RNA sample was extracted in the lab
    • rna_conc: RNA concentration of the sample in ng/uL
    • RQN: RNA quality number measured by a Fragment Analyzer 5200 (Agilent Technology, Inc., Santa Clara, CA)
    • LID_date: Date the library was processed in the lab
    • LID_conc: concentration of the library preparation sample in ng/uL

Details for: biopsies_meta_teeth.csv

  • Description: a comma-delimited file containing the teeth morphometric data for each viable chest biopsy sample (N=36) used to age adults

  • Format(s): .csv

  • Size(s): 2.66 KB

  • Dimensions: 36 rows x 9 columns

  • Variables:

    • LID: Library Identification Number for chest skin biopsy samples
    • age: numerical age of the individual if the DOB is known for that gelada; "unknown" if the individual is not in the demographic data
    • age_cat_teeth: adulthood was determined using the eruption of the third molar; categories include: adult male, adult female, subadult male, subadult female
    • L.up_M3: state of the left upper third molar (M3); categories include: worn, present, not fully erupted, missing
    • L.low_M3: state of the left lower third molar (M3); categories include: worn, present, not fully erupted, missing
    • R.up_M3: state of the right upper third molar (M3); categories include: worn, present, not fully erupted, missing
    • R.low_M3: state of the right lower third molar (M3); categories include: worn, present, not fully erupted, missing
    • teeth.notes: descriptive notes accompanying the third molar (M3); some rows left blank
    • age.notes: descriptive notes accompanying the numerical age; some rows left blank

  • Missing data codes: blank cell

Details for: biopsies_mmul10_gene_chr.csv

  • Description: a comma-delimited file containing the chromosome name/number or scaffold name associated with ensembl gene names used for annotating chromosomal regions

  • Format(s): .csv

  • Size(s): 801.16 KB

  • Dimensions: 35395 rows x 2 columns

  • Variables:

    • gene: ensembl gene name in the Macaque mulatta genome (Mmul_10)
    • chr_scaff_name: associated chromosome number/letter or scaffold name

Details for: biopsies_AR.csv

  • Description: a comma-delimited file containing the proteins that interact with Androgen Receptor (AR) in the Interlogous Interaction Database (http://ophid.utoronto.ca/ophidv2.204/) - Online Predicted Human Interaction (OPHID) database

  • Format(s): .csv

  • Size(s): 8.59 KB

  • Dimensions: 360 rows x 4 columns

  • Variables:

    • UniProt1: UniProt gene name of the query protein (P10275)
    • UniProt2: UniProt gene name of the protein that interacts with Androgen Receptor (AR)
    • symbol1: GeneCards name of the query protein (AR)
    • symbol2: GeneCards name of the protein that interacts with Androgen Receptor (AR)

  • Missing data codes: blank cell

Details for: biopsies_ESR1.csv

  • Description: a comma-delimited file containing the proteins that interact with Estrogen Receptor Alpha (ESR1) in the Interlogous Interaction Database (http://ophid.utoronto.ca/ophidv2.204/) - Online Predicted Human Interaction (OPHID) database

  • Format(s): .csv

  • Size(s): 19.78 KB

  • Dimensions: 758 rows x 4 columns

  • Variables:

    • UniProt1: UniProt gene name of the query protein (P03372)
    • UniProt2: UniProt gene name of the protein that interacts with Estrogen Receptor 1 (ESR1)
    • symbol1: GeneCards name of the query protein (ESR1)
    • symbol2: GeneCards name of the protein that interacts with Estrogen Receptor 1 (ESR1)

Details for: biopsies_ESR2.csv

  • Description: a comma-delimited file containing the proteins that interact with Estrogen Receptor Beta (ESR2) in the Interlogous Interaction Database (http://ophid.utoronto.ca/ophidv2.204/) - Online Predicted Human Interaction (OPHID) database

  • Format(s): .csv

  • Size(s): 16.58 KB

  • Dimensions: 636 rows x 4 columns

  • Variables:

    • UniProt1: UniProt gene name of the query protein (Q92731)
    • UniProt2: UniProt gene name of the protein that interacts with Estrogen Receptor 2 (ESR2)
    • symbol1: GeneCards name of the query protein (ESR2)
    • symbol2: GeneCards name of the protein that interacts with Estrogen Receptor 2 (ESR2)

Details for: biopsies_red_anes_rna.csv

  • Description: a comma-delimited file containing the list of individual's we have both baseline anesthetized redness data and RNA-Seq data (N=18)

  • Format(s): .csv

  • Size(s): 436 bytes

  • Dimensions: 18 rows x 2 columns

  • Variables:

    • LID: Library Identification Number for chest skin biopsy samples
    • rg: chest redness value (numerical ratio of red to green) at baseline temperature while anesthetized (see Methods)

END OF README

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Data and code for the manuscript: "Transcriptional changes capture sex differences in vascularization in a skin coloration signal in a wild primate." Submission to Molecular Ecology.

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