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Data from: Thymic atrophy caused by porcine reproductive and respiratory syndrome virus (PRRSV) infection is pathogenicity-dependent and temporally progressive

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: September 30, 2026 at 09:30 PM | Dataset Last Updated: July 31, 2026
This online resource provides supplementary items used to analyze work in, "Thymic atrophy caused by porcine reproductive and respiratory syndrome virus (PRRSV) infection is pathogenicity-dependent and temporally progressive" by Wiarda et al. Thymus samples were collected from pigs euthanized at 2, 6, and 10 days after inoculation with mock inoculum or one of three PRRSV strains. PRRSVs included MN184, a moderately pathogenic PRRSV recovered from the United States during the early 2000s; L1C.5, a highly pathogenic PRRSV (HP-PRRSV) recovered from the United States in 2021; and JXwn06, a recombinant virus with sequences recovered from a Chinese HP-PRRSV in 2006. Collected thymus samples were submitted for bulk transcriptomics and pathology analysis. Animal meta data, gene count data, pathology results, and additional files and results used to analyze transcriptomics and pathology data are available here.

Resources

13 resources available

  • 20260227_gProfiler_v97archive_GSEA_HallmarkgeneSets_humanToPigOrthologs.xlsx

    XLSX
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  • dddsObject.rds

    RDS
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  • DEGs_CellTypes_Wiarda2025Thymus.xlsx

    XLSX
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  • GSEA_GuThymusGeneSets_AUCScores.xlsx

    XLSX
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  • GSEA_HallmarkGeneSets_AUCScores.xlsx

    XLSX
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  • GSEA_HallmarkGeneSets_HumanToPigOrthos.xlsx

    XLSX
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  • GSEA_WiardaThymusGeneSets_AUCScores.xlsx

    XLSX
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  • SV671_bulkRNAseq_Thymus_GeneCounts_Refined.csv

    CSV
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  • SV671_bulkRNAseq_Thymus_TargetFile_Refined.xlsx

    XLSX
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  • SV671_ThymusPathologyScoring.xlsx

    XLSX
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  • Thy_5999_FindAllMarkers.xlsx

    XLSX
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  • UpdatedGeneNameListForSus97GTF_06302021_JEW_SKS.xlsx

    XLSX
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  • vsdbObject.rds

    RDS
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Complete Metadata
@type dcat:Dataset
accessLevel 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 work in, "Thymic atrophy caused by porcine reproductive and respiratory syndrome virus (PRRSV) infection is pathogenicity-dependent and temporally progressive" by Wiarda et al. Thymus samples were collected from pigs euthanized at 2, 6, and 10 days after inoculation with mock inoculum or one of three PRRSV strains. PRRSVs included MN184, a moderately pathogenic PRRSV recovered from the United States during the early 2000s; L1C.5, a highly pathogenic PRRSV (HP-PRRSV) recovered from the United States in 2021; and JXwn06, a recombinant virus with sequences recovered from a Chinese HP-PRRSV in 2006. Collected thymus samples were submitted for bulk transcriptomics and pathology analysis. Animal meta data, gene count data, pathology results, and additional files and results used to analyze transcriptomics and pathology data are available here.</p>
distribution 
[
  {
    "@type": "dcat:Distribution",
    "title": "20260227_gProfiler_v97archive_GSEA_HallmarkgeneSets_humanToPigOrthologs.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979031"
  },
  {
    "@type": "dcat:Distribution",
    "title": "dddsObject.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/62979052"
  },
  {
    "@type": "dcat:Distribution",
    "title": "DEGs_CellTypes_Wiarda2025Thymus.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979055"
  },
  {
    "@type": "dcat:Distribution",
    "title": "GSEA_GuThymusGeneSets_AUCScores.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979058"
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  {
    "@type": "dcat:Distribution",
    "title": "GSEA_HallmarkGeneSets_AUCScores.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979064"
  },
  {
    "@type": "dcat:Distribution",
    "title": "GSEA_HallmarkGeneSets_HumanToPigOrthos.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979070"
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  {
    "@type": "dcat:Distribution",
    "title": "GSEA_WiardaThymusGeneSets_AUCScores.xlsx",
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    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979073"
  },
  {
    "@type": "dcat:Distribution",
    "title": "SV671_bulkRNAseq_Thymus_GeneCounts_Refined.csv",
    "format": "csv",
    "mediaType": "text/csv",
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  },
  {
    "@type": "dcat:Distribution",
    "title": "SV671_bulkRNAseq_Thymus_TargetFile_Refined.xlsx",
    "format": "xlsx",
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  {
    "@type": "dcat:Distribution",
    "title": "SV671_ThymusPathologyScoring.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979082"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Thy_5999_FindAllMarkers.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979085"
  },
  {
    "@type": "dcat:Distribution",
    "title": "UpdatedGeneNameListForSus97GTF_06302021_JEW_SKS.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/62979091"
  },
  {
    "@type": "dcat:Distribution",
    "title": "vsdbObject.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/62979094"
  }
]
identifier 10.15482/USDA.ADC/31820905.v1
keyword 
[
  "ARS",
  "DEG",
  "DGE",
  "Gene set enrichement analysis",
  "HP-PRRSV",
  "NP103",
  "National Animal Disease Center",
  "PRRS",
  "PRRSV",
  "Porcine Reproductive and Respiratory Syndrome (PRRS)",
  "Porcine reproductive and respiratory syndrome virus (PRRSV)",
  "QuantSeq",
  "QuantSeq 3′",
  "RNA-seq",
  "Swine -- Diseases",
  "USDA",
  "atrophy",
  "data.gov",
  "differential gene expression",
  "differentially expressed gene",
  "disease",
  "gene set",
  "gene set enrichment",
  "gene set enrichment analyses (GSEA)",
  "gene signature",
  "immune",
  "immune development",
  "infection",
  "pathology",
  "pig",
  "pigs",
  "porcine",
  "porcine reproductive and respiratory swine virus",
  "porcine reproductive and respiratory syndrome",
  "porcine reproductive and respiratory syndrome virus 2",
  "swine",
  "thymi",
  "thymic atrophy",
  "thymus",
  "thymus atrophy",
  "transcriptomics"
]
license https://creativecommons.org/licenses/by/4.0/
modified 2026-07-31
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2024-06-19/2024-06-28
title Data from: Thymic atrophy caused by porcine reproductive and respiratory syndrome virus (PRRSV) infection is pathogenicity-dependent and temporally progressive

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