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Data from: A single-cell immune atlas of primary and secondary lymphoid organs in pigs

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: August 01, 2026 at 04:52 AM | Dataset Last Updated: March 09, 2026
Data objects used for analysis in "A single-cell immune atlas of primary and secondary lymphoid organs in pigs" by Wiarda et al. Data objects include .cloupe files for interactive query in Loupe Cell Browser (10X Genomics), .rds files to download for use with a Shiny app for data query, and .h5seurat files for computational query of data. Briefly, cells were isolated from bone marrow, thymus, lymph node, and spleen of two pigs and processed for single-cell RNA sequencing. Single-cell RNA sequencing data was analyzed to identify cell types in each tissue and perform comparisons across tissues and across datasets.

Resources

18 resources available

  • sp.cloupe

    CLOUPE
    Download

  • bm.cloupe

    CLOUPE
    Download

  • ln.cloupe

    CLOUPE
    Download

  • th.cloupe

    CLOUPE
    Download

  • PigImmuneMultiTissue_Spleen_CellTypeAnnotated_HBBhiRemoved.h5Seurat

    H5SEURAT
    Download

  • PigImmuneMultiTissue_AllTissues_CellTypeMerge_Myeloid.h5Seurat

    H5SEURAT
    Download

  • PigImmuneMultiTissue_BoneMarrow_CellTypeAnnotated_HBBhiRemoved.h5Seurat

    H5SEURAT
    Download

  • PigImmuneMultiTissue_AllTissues_CellTypeMerge_B.h5Seurat

    H5SEURAT
    Download

  • PigImmuneMultiTissue_LymphNode_CellTypeAnnotated.h5Seurat

    H5SEURAT
    Download

  • PigImmuneMultiTissue_Thymus_CellTypeAnnotated.h5Seurat

    H5SEURAT
    Download

  • PigImmuneMultiTissue_AllTissues_CellTypeMerge_TILC.h5Seurat

    H5SEURAT
    Download

  • Thymus_shiny.rds

    RDS
    Download

  • Lymph_Node_mapped_shiny.rds

    RDS
    Download

  • Spleen_shiny.rds

    RDS
    Download

  • Spleen_mapped_shiny.rds

    RDS
    Download

  • Thymus_mapped_shiny.rds

    RDS
    Download

  • Bone_Marrow_shiny.rds

    RDS
    Download

  • Lymph_Node_shiny.rds

    RDS
    Download

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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">Data objects used for analysis in "A single-cell immune atlas of primary and secondary lymphoid organs in pigs" by Wiarda et al. Data objects include .cloupe files for interactive query in Loupe Cell Browser (10X Genomics), .rds files to download for use with a Shiny app for data query, and .h5seurat files for computational query of data. Briefly, cells were isolated from bone marrow, thymus, lymph node, and spleen of two pigs and processed for single-cell RNA sequencing. Single-cell RNA sequencing data was analyzed to identify cell types in each tissue and perform comparisons across tissues and across datasets.</p>
distribution 
[
  {
    "@type": "dcat:Distribution",
    "title": "sp.cloupe",
    "format": "cloupe",
    "mediaType": "application/json",
    "downloadURL": "https://ndownloader.figshare.com/files/56031182"
  },
  {
    "@type": "dcat:Distribution",
    "title": "bm.cloupe",
    "format": "cloupe",
    "mediaType": "application/json",
    "downloadURL": "https://ndownloader.figshare.com/files/56031185"
  },
  {
    "@type": "dcat:Distribution",
    "title": "ln.cloupe",
    "format": "cloupe",
    "mediaType": "application/json",
    "downloadURL": "https://ndownloader.figshare.com/files/56031188"
  },
  {
    "@type": "dcat:Distribution",
    "title": "th.cloupe",
    "format": "cloupe",
    "mediaType": "application/json",
    "downloadURL": "https://ndownloader.figshare.com/files/56031191"
  },
  {
    "@type": "dcat:Distribution",
    "title": "PigImmuneMultiTissue_Spleen_CellTypeAnnotated_HBBhiRemoved.h5Seurat",
    "format": "h5Seurat",
    "mediaType": "application/x-hdf",
    "downloadURL": "https://ndownloader.figshare.com/files/56031206"
  },
  {
    "@type": "dcat:Distribution",
    "title": "PigImmuneMultiTissue_AllTissues_CellTypeMerge_Myeloid.h5Seurat",
    "format": "h5Seurat",
    "mediaType": "application/x-hdf",
    "downloadURL": "https://ndownloader.figshare.com/files/56031209"
  },
  {
    "@type": "dcat:Distribution",
    "title": "PigImmuneMultiTissue_BoneMarrow_CellTypeAnnotated_HBBhiRemoved.h5Seurat",
    "format": "h5Seurat",
    "mediaType": "application/x-hdf",
    "downloadURL": "https://ndownloader.figshare.com/files/56031215"
  },
  {
    "@type": "dcat:Distribution",
    "title": "PigImmuneMultiTissue_AllTissues_CellTypeMerge_B.h5Seurat",
    "format": "h5Seurat",
    "mediaType": "application/x-hdf",
    "downloadURL": "https://ndownloader.figshare.com/files/56031218"
  },
  {
    "@type": "dcat:Distribution",
    "title": "PigImmuneMultiTissue_LymphNode_CellTypeAnnotated.h5Seurat",
    "format": "h5Seurat",
    "mediaType": "application/x-hdf",
    "downloadURL": "https://ndownloader.figshare.com/files/56031224"
  },
  {
    "@type": "dcat:Distribution",
    "title": "PigImmuneMultiTissue_Thymus_CellTypeAnnotated.h5Seurat",
    "format": "h5Seurat",
    "mediaType": "application/x-hdf",
    "downloadURL": "https://ndownloader.figshare.com/files/56031227"
  },
  {
    "@type": "dcat:Distribution",
    "title": "PigImmuneMultiTissue_AllTissues_CellTypeMerge_TILC.h5Seurat",
    "format": "h5Seurat",
    "mediaType": "application/x-hdf",
    "downloadURL": "https://ndownloader.figshare.com/files/56031251"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Thymus_shiny.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/57194999"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lymph_Node_mapped_shiny.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/57195005"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Spleen_shiny.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/57195008"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Spleen_mapped_shiny.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/57195011"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Thymus_mapped_shiny.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/57195014"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Bone_Marrow_shiny.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/57195017"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lymph_Node_shiny.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/57195056"
  }
]
identifier 10.15482/USDA.ADC/29492726.v1
keyword 
[
  "B cell",
  "DC",
  "ILC",
  "NK cell",
  "NP103",
  "NP108",
  "PIGGI",
  "RNA sequencing",
  "Shiny app",
  "Shiny-PIGGI",
  "ShinyPIGGI",
  "T cell",
  "atlas",
  "biomedical model",
  "bone marrow",
  "cDC",
  "dendritic cell",
  "follicle",
  "germinal center",
  "immune",
  "immunity",
  "innate lymphoid cell",
  "lymph node",
  "macrophage",
  "monocyte",
  "myeloid",
  "natural killer cell",
  "pDC",
  "pig",
  "porcine",
  "progenitor",
  "scRNA-seq",
  "single-cell",
  "spleen",
  "swine",
  "thymocyte",
  "thymus",
  "tissue"
]
license https://creativecommons.org/licenses/by-sa/4.0/
modified 2026-03-09
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2018-01-01/2018-01-01
title Data from: A single-cell immune atlas of primary and secondary lymphoid organs in pigs

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