Regional epithelial cell diversity in the small intestine of pigs

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 https://github.com/USDA-FSEPRU/scRNAseqEpSI_Pilot. Raw data are available at GEO accession GSE208613. Data are available for online query at https://singlecell.broadinstitute.org/single_cell/study/SCP1936/regional....

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.h5Seurat object - epithelial cellsData
Epithelial cells used for data analysis, available in .h5Seurat file format...
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Field	Value
Tags	Pig intestine scRNA-seq epithelial epithelium single-cell RNA sequencing single-cell BEST4 enterocyte enteroendocrine enterochromaffin NP108
Modified	2022-10-06
Release Date	2022-09-29
Identifier	1917800b-a78d-403c-89d4-11b6737704fa
Spatial / Geographical Coverage Area	POLYGON ((-93.581439973495 42.034851789973, -93.581439973495 42.053922832501, -93.569766999863 42.053922832501, -93.569766999863 42.034851789973))
Publisher	Ag Data Commons
Spatial / Geographical Coverage Location	Ames, Iowa
Temporal Coverage	September 26, 2019
License	Creative Commons Attribution Share-Alike
Contact Name	Loving, Crystal
Contact Email	crystal.loving@usda.gov
Public Access Level	Public
Program Code	005:040 - Department of Agriculture - National Research
Bureau Code	005:18 - Agricultural Research Service

Extended Metadata:

Field	Value
Authors	Wiarda, Jayne E. (ORCID) Becker, Sage R. (ORCID) Sivasankaran, Sathesh K. (ORCID) Loving, Crystal L. (ORCID)
Peer Reviewed	No
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.
Funding Sources	Agricultural Research Service 5030-31320-004-00D
Primary Article	Wiarda, J. E., Becker, S. R., Sivasankaran, S. K., & Loving, C. L. (2022). Regional epithelial cell diversity in the small intestine of pigs. Journal of Animal Science. https://doi.org/10.1093/jas/skac318
Related Articles	Wiarda, J. E., Trachsel, J. M., Sivasankaran, S. K., Tuggle, C. K., & Loving, C. L. (2022). Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells. Life Science Alliance, 5(10), e202201442. https://doi.org/10.26508/lsa.202201442 Herrera-Uribe, J., Wiarda, J. E., Sivasankaran, S. K., Daharsh, L., Liu, H., Byrne, K. A., Smith, T. P. L., Lunney, J. K., Loving, C. L., & Tuggle, C. K. (2021). Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing. Frontiers in Genetics, 12. https://doi.org/10.3389/fgene.2021.689406 Elmentaite, R., Kumasaka, N., Roberts, K., Fleming, A., Dann, E., King, H. W., Kleshchevnikov, V., Dabrowska, M., Pritchard, S., Bolt, L., Vieira, S. F., Mamanova, L., Huang, N., Perrone, F., Goh Kai’En, I., Lisgo, S. N., Katan, M., Leonard, S., Oliver, T. R. W., … Teichmann, S. A. (2021). Cells of the human intestinal tract mapped across space and time. Nature, 597(7875), 250-255. https://doi.org/10.1038/s41586-021-03852-1 Haber, A. L., Biton, M., Rogel, N., Herbst, R. H., Shekhar, K., Smillie, C., Burgin, G., Delorey, T. M., Howitt, M. R., Katz, Y., Tirosh, I., Beyaz, S., Dionne, D., Zhang, M., Raychowdhury, R., Garrett, W. S., Rozenblatt-Rosen, O., Shi, H. N., Yilmaz, O., … Regev, A. (2017). A single-cell survey of the small intestinal epithelium. Nature, 551(7680), 333-339. https://doi.org/10.1038/nature24489 Li, H., Wang, X., Wang, Y., Zhang, M., Hong, F., Wang, H., Cui, A., Zhao, J., Ji, W., & Chen, Y.-G. (2022). Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium. Cell Regeneration, 11(1). https://doi.org/10.1186/s13619-022-00118-7 Meng, Q., Chen, L., Xiong, B., Kang, B., Zhang, P., Tang, S., Han, H., Shen, W., Feng, X., Feng, S., Zhong, R., Tang, X., Zhang, S., Zhang, H., & Zhao, Y. (2021). Single-Cell Transcriptome Sequencing and Proteomics Reveal Neonatal Ileum Dynamic Developmental Potentials. MSystems, 6(5). https://doi.org/10.1128/msystems.00725-21 Tang, W., Zhong, Y., Wei, Y., Deng, Z., Mao, J., Liu, J., Valencak, T. G., Liu, J., Xu, H., & Wang, H. (2022). Ileum tissue single-cell mRNA sequencing elucidates the cellular architecture of pathophysiological changes associated with weaning in piglets. BMC Biology, 20(1). https://doi.org/10.1186/s12915-022-01321-3
Method Citation	Herrera-Uribe, J., Wiarda, J. E., Sivasankaran, S. K., Daharsh, L., Liu, H., Byrne, K. A., Smith, T. P. L., Lunney, J. K., Loving, C. L., & Tuggle, C. K. (2021). Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing. Frontiers in Genetics, 12. https://doi.org/10.3389/fgene.2021.689406 Wiarda, J. E., Trachsel, J. M., Sivasankaran, S. K., Tuggle, C. K., & Loving, C. L. (2022). Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells. Life Science Alliance, 5(10), e202201442. https://doi.org/10.26508/lsa.202201442
Dataset DOI (digital object identifier)	10.15482/USDA.ADC/1527979

Field	Value
OSTI Identifier
ISO Topic(s)	farming health
State or Territory	Iowa
National Agricultural Library Thesaurus Term	epithelial cells duodenum jejunum ileum swine sequence analysis transcriptomics gene expression epithelium
Ag Data Commons Keywords	Animals & Livestock Animal health Animals & Livestock Genomics & Genetics Transcriptome Genomics & Genetics Food & Nutrition Food safety Food & Nutrition

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