sorry, we can't preview this file
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-epithelial-cell-diversity-in-the-small-intestine-of-pigs.
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.
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 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
2019-09-26Theme
- Not specified
Geographic Coverage
{"type":"FeatureCollection","features":[{"geometry":{"type":"Polygon","coordinates":[[[-93.581439973495,42.034851789973],[-93.581439973495,42.053922832501],[-93.569766999863,42.053922832501],[-93.569766999863,42.034851789973],[-93.581439973495,42.034851789973]]]},"type":"Feature","properties":{}}]}Geographic location - description
Ames, IowaISO Topic Category
- farming
- health
National Agricultural Library Thesaurus terms
epithelial cells; duodenum; jejunum; ileum; swine; sequence analysis; transcriptomics; gene expression; epitheliumOMB 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
