Skip to main content
U.S. flag

An official website of the United States government

This site is currently in beta, and your feedback is helping shape its ongoing development.

Return to search results

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

Published by Agricultural Research Service | Department of Agriculture | Metadata Last Checked: January 27, 2026 | Last Modified: 2025-09-08
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

Find Related Datasets

Click any tag below to search for similar datasets

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 2025-09-08
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

data.gov

An official website of the GSA's Technology Transformation Services

Looking for U.S. government information and services?
Visit USA.gov