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Series GSE196388 Query DataSets for GSE196388
Status Public on Aug 19, 2022
Title Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing
Organism Sus scrofa
Experiment type Expression profiling by high throughput sequencing
Summary Intestinal lymphocytes are crucial members of the mucosal immune system with impact over outcomes of intestinal health versus dysbiosis. Resolving intestinal lymphocyte complexity and function is a challenge, as the intestine provides cellular snapshots of a diverse spectrum of immune states. In pigs, intestinal lymphocytes are poorly described relative to humans or traditional model species. Enhanced understanding of porcine intestinal lymphocytes will promote food security and improve utility of pigs as a biomedical model for intestinal research. Single-cell RNA sequencing (scRNA-seq) was performed to provide transcriptomic profiles of lymphocytes in porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation revealed previously undescribed cells in porcine intestine, including SELLhi gd T cells, group 1 and group 3 innate lymphoid cells (ILCs), and four subsets of B cells. Single-cell transcriptomes in ileum were compared to those in porcine blood, and subsets of activated lymphocytes were detected in ileum but not periphery. Comparison to scRNA-seq human and murine ileum data revealed a general consensus of ileal lymphocytes across species. Lymphocyte spatial context in porcine ileum was conferred through differential tissue dissection prior to scRNA-seq. Antibody-secreting cells, B cells, follicular CD4 ab T cells, and cycling T/ILCs were enriched in ileum with Peyer’s patches, while non-cycling gd T, CD8 ab T, and group 1 ILCs were enriched in ileum without Peyer’s patches. scRNA-seq findings were leveraged to develop advanced toolsets for further identification of ILCs in porcine ileum via flow cytometry and in situ staining. Porcine ileal ILCs identified via scRNA-seq did not transcriptionally mirror peripheral porcine ILCs (corresponding to natural killer cells) but instead had gene signatures indicative of tissue- and activation-specific functions, indicating potentially similar roles to intestinal ILCs identified in humans. Overall, the data serve as a highly-resolved transcriptomic atlas of the porcine intestinal immune landscape and will be useful in further understanding intestinal immune cell function.
Overall design Ileum was collected from each of two seven-week-old pigs and dissected into three sample types: (1) ileum containing only regions with Peyer’s patches (PP), (2) ileum containing only regions without Peyer’s patches (non-PP), and (3) ileum representative of a transverse cross section containing both regions with and without Peyer’s patches (whole ileum). From each of the six ileum samples, cells were isolated from combined epithelium, lamina propria, and submucosa and enriched for viable lymphocytes. In parallel, PBMC samples were collected for the same two pigs and processed to obtain single-cell suspensions. Sequences used in htis stduy were deposited to the NCBI SRA and can be fount using the identifier PRJNA802582.
Contributor(s) Wiarda JE, Trachsel JM, Sivasankaran SK, Tuggle CK, Loving CL
Citation(s) 35995567
BioProject PRJNA802582
Submission date Feb 08, 2022
Last update date Sep 15, 2022
Contact name Sathesh K Sivasankaran
Organization name University of Missouri
Lab Bioinformatics and Analytics Core
Street address Bond Life Sciences Center Suite 106, 1201 Rollins Street
City Columbia
State/province MO
ZIP/Postal code 65211
Country USA
Platforms (1)
GPL24486 Illumina HiSeq 3000 (Sus scrofa)
Samples (32)
GSM5879997 Nopp1-1
GSM5879998 Nopp1-2
GSM5879999 Nopp1-3

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE196388_NoPP1_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE196388_NoPP1_features.tsv.gz 238.9 Kb (ftp)(http) TSV
GSE196388_NoPP1_matrix.mtx.gz 42.6 Mb (ftp)(http) MTX
GSE196388_NoPP2_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE196388_NoPP2_features.tsv.gz 238.9 Kb (ftp)(http) TSV
GSE196388_NoPP2_matrix.mtx.gz 40.0 Mb (ftp)(http) MTX
GSE196388_PBMC1_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE196388_PBMC1_features.tsv.gz 238.9 Kb (ftp)(http) TSV
GSE196388_PBMC1_matrix.mtx.gz 46.3 Mb (ftp)(http) MTX
GSE196388_PBMC2_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE196388_PBMC2_features.tsv.gz 238.9 Kb (ftp)(http) TSV
GSE196388_PBMC2_matrix.mtx.gz 53.8 Mb (ftp)(http) MTX
GSE196388_PP1_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE196388_PP1_features.tsv.gz 238.9 Kb (ftp)(http) TSV
GSE196388_PP1_matrix.mtx.gz 63.6 Mb (ftp)(http) MTX
GSE196388_PP2_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE196388_PP2_features.tsv.gz 238.9 Kb (ftp)(http) TSV
GSE196388_PP2_matrix.mtx.gz 52.2 Mb (ftp)(http) MTX
GSE196388_WholeIleum1_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE196388_WholeIleum1_features.tsv.gz 238.9 Kb (ftp)(http) TSV
GSE196388_WholeIleum1_matrix.mtx.gz 47.5 Mb (ftp)(http) MTX
GSE196388_WholeIleum2_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE196388_WholeIleum2_features.tsv.gz 238.9 Kb (ftp)(http) TSV
GSE196388_WholeIleum2_matrix.mtx.gz 54.5 Mb (ftp)(http) MTX
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