Conserved B cell signaling, activation, and differentiation in porcine jejunal and ileal Peyer's patches despite distinct immune landscapes
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).
See README for list of resources in this dataset with descriptions.
Funding
USDA-ARS: 5030-31320-004-00D
History
Data contact name
Loving, CrystalData contact email
crystal.loving@usda.govPublisher
Ag Data CommonsIntended 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
2020-04-01Theme
- Not specified
Geographic Coverage
{"type":"FeatureCollection","features":[{"geometry":{"type":"Point","coordinates":[-93.576693534851,42.045130793063]},"type":"Feature","properties":{}}]}Geographic location - description
1920 Dayton Avenue, Ames, Iowa 50010ISO 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; chromiumOMB 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
