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Data from: Porcine epidemic diarrhea virus infection promotes Peyer’s patch immune induction and epithelial defense via single-cell transcriptional reprogramming

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: October 09, 2026 at 04:38 PM | Dataset Last Updated: August 28, 2026
This online resource provides supplementary items used to analyze data in the work, "Porcine epidemic diarrhea virus infection promotes Peyer's patch immune induction and epithelial defense via single-cell transcriptional reprogramming" by Wiarda et al. Four-week-old pigs were inoculated with 2 mL of 105 TCID50/mL of porcine epidemic diarrhea virus (PEDV) non-S-INDEL isolate USA/NC49469/2013 (n=5) or mock inoculum (n=3). At 5 days post-inoculation, tissue was collected from the site with the proximal-most jejunal Peyer's patch, cells were isolated, and samples were submitted for single-cell RNA sequencing (scRNA-seq). Analyzed scRNA-seq data yielded a dataset of 40,522 total cells derived from eight animal samples. Cells were further annotated into 43 clusters, 29 cell types, and five cell lineages. Four of five PEDV pigs had successful PEDV infection in the jejunum tissue harvested for scRNA-seq and were used for comparisons to the three mock animals. Computational data objects of total cell and epithelial cell datasets are included here (.h5seurat objects), as well as data objects used for trajectory analysis and cell interaction analysis (saved as .rds files). Files that can be used for non-computational, interactive dataset query with freely accessible software (.cloupe files, compatible with Loupe Browser software [10X Genomics]) are also available.

Resources

11 resources available

  • GSEA_HallmarkGeneSets_HumanToPigOrthos (1).xlsx

    XLSX
    Download

  • cellchat_TreatmentsMerged_AllSignaling.rds

    RDS
    Download

  • UpdatedGeneNameListForSus97GTF_06302021_JEW_SKS.xlsx

    XLSX
    Download

  • PigToHuman_GeneOrthos_v97.txt

    TXT
    Download

  • slingshot_PolarizedEnterocytes.rds

    RDS
    Download

  • pseudotime_GAM_model_Epithelial.rds

    RDS
    Download

  • slingshot_Epithelial.rds

    RDS
    Download

  • cellchatMock_AllSignaling.rds

    RDS
    Download

  • cellchatPEDV_AllSignaling.rds

    RDS
    Download

  • Sus_scrofa.Sscrofa11.1.97_modified06302021_JEW_SKS_PEDV_USA_NC_2013_49469.gtf

    GTF
    Download

  • AllSamples_Annotated.h5Seurat.zip

    ZIP
    Download

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Complete Metadata
@type dcat:Dataset
accessLevel public
accessRights public
bureauCode 
[
  "005:18"
]
contactPoint 
{
  "fn": "Wiarda, Jayne, E.",
  "hasEmail": "mailto:jayne.wiarda@usda.gov"
}
description <p dir="ltr">This online resource provides supplementary items used to analyze data in the work, "Porcine epidemic diarrhea virus infection promotes Peyer's patch immune induction and epithelial defense via single-cell transcriptional reprogramming" by Wiarda et al. Four-week-old pigs were inoculated with 2 mL of 10<sup>5 </sup>TCID<sub>50</sub>/mL of porcine epidemic diarrhea virus (PEDV) non-S-INDEL isolate USA/NC49469/2013 (n=5) or mock inoculum (n=3). At 5 days post-inoculation, tissue was collected from the site with the proximal-most jejunal Peyer's patch, cells were isolated, and samples were submitted for single-cell RNA sequencing (scRNA-seq). Analyzed scRNA-seq data yielded a dataset of 40,522 total cells derived from eight animal samples. Cells were further annotated into 43 clusters, 29 cell types, and five cell lineages. Four of five PEDV pigs had successful PEDV infection in the jejunum tissue harvested for scRNA-seq and were used for comparisons to the three mock animals. Computational data objects of total cell and epithelial cell datasets are included here (.h5seurat objects), as well as data objects used for trajectory analysis and cell interaction analysis (saved as .rds files). Files that can be used for non-computational, interactive dataset query with freely accessible software (.cloupe files, compatible with Loupe Browser software [10X Genomics]) are also available.</p>
distribution 
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  {
    "@type": "dcat:Distribution",
    "title": "GSEA_HallmarkGeneSets_HumanToPigOrthos (1).xlsx",
    "format": "xlsx",
    "license": "https://creativecommons.org/licenses/by/4.0/",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/67704522"
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  {
    "@type": "dcat:Distribution",
    "title": "cellchat_TreatmentsMerged_AllSignaling.rds",
    "format": "rds",
    "license": "https://creativecommons.org/licenses/by/4.0/",
    "mediaType": "application/gzip",
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  },
  {
    "@type": "dcat:Distribution",
    "title": "UpdatedGeneNameListForSus97GTF_06302021_JEW_SKS.xlsx",
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    "title": "PigToHuman_GeneOrthos_v97.txt",
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    "license": "https://creativecommons.org/licenses/by/4.0/",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/67704531"
  },
  {
    "@type": "dcat:Distribution",
    "title": "slingshot_PolarizedEnterocytes.rds",
    "format": "rds",
    "license": "https://creativecommons.org/licenses/by/4.0/",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/67704534"
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    "@type": "dcat:Distribution",
    "title": "pseudotime_GAM_model_Epithelial.rds",
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    "mediaType": "application/gzip",
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    "format": "rds",
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    "mediaType": "application/gzip",
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  {
    "@type": "dcat:Distribution",
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  {
    "@type": "dcat:Distribution",
    "title": "cellchatPEDV_AllSignaling.rds",
    "format": "rds",
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    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/67704546"
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  {
    "@type": "dcat:Distribution",
    "title": "Sus_scrofa.Sscrofa11.1.97_modified06302021_JEW_SKS_PEDV_USA_NC_2013_49469.gtf",
    "format": "gtf",
    "license": "https://creativecommons.org/licenses/by/4.0/",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/67704549"
  },
  {
    "@type": "dcat:Distribution",
    "title": "AllSamples_Annotated.h5Seurat.zip",
    "format": "zip",
    "license": "https://creativecommons.org/licenses/by/4.0/",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/67704564"
  }
]
identifier 10.15482/USDA.ADC/28986395.v1
keyword 
[
  "ARS",
  "NP103",
  "National Animal Disease Center",
  "PED",
  "PEDV",
  "Peyer's patch",
  "Peyer's patches",
  "Porcine epidemic diarrhea (PED)",
  "RNA-seq",
  "Swine -- Diseases",
  "USDA",
  "cell",
  "data.gov",
  "enterocyte",
  "enterocytes",
  "epithelial",
  "epithelium",
  "gene",
  "gene signature",
  "immune",
  "jejunum",
  "pig",
  "pigs",
  "porcine",
  "porcine epidemic diarrhea virus",
  "porcine epidemic diarrhea virus Porcine epidemic diarrhea",
  "scRNA-seq",
  "single-cell",
  "source code",
  "swine"
]
license https://creativecommons.org/licenses/by/4.0/
modified 2026-08-28
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 
[
  {
    "@type": "PeriodOfTime",
    "endDate": "2024-06-25",
    "startDate": "2024-06-25"
  }
]
title Data from: Porcine epidemic diarrhea virus infection promotes Peyer’s patch immune induction and epithelial defense via single-cell transcriptional reprogramming

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