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