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Conserved B cell signaling, activation, and differentiation in porcine jejunal and ileal Peyer's patches despite distinct immune landscapes

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posted on 2024-02-23, 18:46 authored by Jayne WiardaJayne Wiarda, Adrienne L. Shircliff, Judith B. Stasko, Sathesh K. Sivasankaran, Mark R. Ackermann, Crystal L. Loving
<p>This dataset contains files used in the manuscript, "Conserved B cell signaling, activation, and differentiation in porcine jejunal and ileal Peyer's patches despite distinct immune landscapes" by Wiarda et al. (2023). Samples of jejunum and ileum containing Peyer's patches were collected from each of three, 8-week-old, female pigs and processed for single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (STomics). Data were analyzed to determine cell type compositions, spatial regions, gene expression, signaling interaction networks, activation trajectories, and cell locations. Files included here can be used to reconstruct all analyses of the manuscript, allowing individual users to perform independent queries. Also included is a vignette of all coding steps used in this work, provided as a Markdown file. Scripts and raw data will be available via preprint (to follow).</p> <p>See README for list of resources in this dataset with descriptions.</p>

Funding

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

History

Related Materials

  1. 1.
    DOI - Is supplemented by 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
  2. 2.
    DOI - Is supplemented by 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, 101. https://doi.org/10.1093/jas/skac318
  3. 3.
    DOI - Is supplemented by 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
  4. 4.
    DOI - Is supplement to Wiarda, J. E., Shircliff, A. L., Becker, S. R., Stasko, J. B., Sivasankaran, S. K., Ackermann, M. R., & Loving, C. L. (2024). Conserved B cell signaling, activation, and differentiation in porcine jejunal and ileal Peyer’s patches despite distinct immune landscapes. Mucosal Immunology. https://doi.org/10.1016/j.mucimm.2024.08.005

Data contact name

Loving, Crystal

Data contact email

crystal.loving@usda.gov

Publisher

Ag Data Commons

Intended use

Single-cell RNA sequencing data and spatial transcriptomics data from porcine ileum and jejunum may be used to query transcriptional profiles of cell populations and spatial regions, respectively.

Use limitations

Single-cell RNA sequencing and spatial transcriptomics data includes sparse data, making it difficult to pinpoint whether some genes are lowly expressed but not detected versus not expressed. Some level of ambient RNA contamination is also expected in cells/regions. The single-cell RNA sequencing dataset includes cells enriched for lymphocytes and is thus not representative of total cell type proportions in the original tissue.

Temporal Extent Start Date

2020-04-01

Theme

  • Not specified

Geographic Coverage

Geographic location - description

1920 Dayton Avenue, Ames, Iowa 50010

ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

B-lymphocytes; swine; jejunum; ileum; Peyer's patches; immunity; data collection; females; sequence analysis; transcriptomics; data analysis; gene expression; chromium

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.; Shircliff, Adrienne L.; Stasko, Judith B.; Sivasankaran, Sathesh K.; Ackermann, Mark R.; Loving, Crystal L. (2023). Conserved B cell signaling, activation, and differentiation in porcine jejunal and ileal Peyer's patches despite distinct immune landscapes. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1529557

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    Categories

    Keywords

    single-cellsingle-cell RNA sequencingspatial transcriptomicsspatialtrancriptomicsVisiumchromium10XPigPorcineB cellB cell subpopulationsSwineNP108RNA sequencingRNA-SeqscRNA-seqSTomicsintestinePeyer's patchimmuneleukocyteleukocytesPorcine leukocyteslymphocytejejunumileumdata.govARS

    Licence

    CC BY-SA 4.0

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