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Regional epithelial cell diversity in the small intestine of pigs

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posted on 2024-02-21, 19:18 authored by Jayne WiardaJayne Wiarda, Sage R. Becker, Sathesh K. Sivasankaran, Crystal L. Loving

Single cell suspensions enriched for epithelial cells were obtained from duodenum, jejunum, and ileum of a 7.5-week-old pig and subjected to single-cell RNA sequencing (scRNA-seq). scRNA-seq was performed to provide transcriptomic profiles of epithelial cells, with 695 cells annotated into 6 cell types. Deeper interrogation of data revealed previously undescribed cells in porcine intestine, and region-specific gene expression profiles within specific cell subsets. Data herein includes a .h5seurat files of the epithelial cell subsets analyzed. Files may be used to reconstruct different analyses and perform further data query. Scripts for original data analyses are found at Raw data are available at GEO accession GSE208613. Data are available for online query at

Resources in this dataset:

  • Resource Title: .h5Seurat object - epithelial cells.

    File Name: EpithelialCells.tar

    Resource Description: Epithelial cells used for data analysis, available in .h5Seurat file format. Untar file before use.


USDA-ARS: 5030-31320-004-00D


Data contact name

Loving, Crystal

Data contact email


Ag Data Commons

Intended use

Single-cell RNA sequencing data may be used to query gene expression profiles of epithelial cells derived from various locations within the small intestine of pigs.

Use limitations

Single-cell RNA sequencing data includes sparse data, making it difficult to pinpoint whether some genes are lowly expressed but not detected versus not expressed. This dataset includes cells from only one animal. Technical factors including cell isolation and data analysis could potentially affect recovery of certain cell populations, so cell type frequency data should be interpreted cautiously.

Temporal Extent Start Date



  • Not specified

Geographic Coverage


Geographic location - description

Ames, Iowa

ISO Topic Category

  • farming
  • health

National Agricultural Library Thesaurus terms

epithelial cells; duodenum; jejunum; ileum; swine; sequence analysis; transcriptomics; gene expression; epithelium

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 108

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Wiarda, Jayne E.; Becker, Sage R.; Sivasankaran, Sathesh K.; Loving, Crystal L. (2022). Regional epithelial cell diversity in the small intestine of pigs. Ag Data Commons.