Data from: Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing

Files pertaining to data analyses performed and presented in the preprint, 'Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing' by Wiarda et al. 2022 are provided in this dataset. Single cell suspensions enriched for lymphocytes were obtained from ileum of two seven-week-old pigs and subjected to single-cell RNA sequencing (scRNA-seq). Peripheral blood mononuclear cells (PBMCs) were collected and processed for scRNA-seq in parallel. scRNA-seq was performed to provide transcriptomic profiles of lymphocytes in porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation of data revealed previously undescribed cells in porcine intestine, including SELLhi γδ 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 αβ T cells, and cycling T/ILCs were enriched in ileum with Peyer’s patches, while non-cycling γδ T, CD8 αβ T, and group 1 ILCs were enriched in ileum without Peyer’s patches. Data files included herein are .h5seurat files of the various cell subsets included in analyses of the manuscript. 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/scRNAseq_Porcine_Ileum_PBMC. Raw data are available at GEO accession GSE196388. Data are available for online query at https://singlecell.broadinstitute.org/single_cell/study/SCP1921/intestinal-single-cell-atlas-reveals-novel-lymphocytes-in-pigs-with-similarities-to-human-cells. Resources in this dataset:Resource Title: Ileum_AllCells. File Name: Ileum_AllCells.tarResource Description: .h5seurat object of all the cells derived from ileum samples. Untar into .h5seurat file before use.Resource Title: GutBlood_IntegratedILCs. File Name: GutBlood_IntegratedILCs.tarResource Description: .h5seurat object of ILCs derived from both ileum and PBMC samples. Untar into .h5seurat file before use.Resource Title: Ileum_Bonly. File Name: Ileum_Bonly.tarResource Description: .h5seurat object of B cells and antibody-secreting cells derived from ileum samples. Untar into .h5seurat file before use.Resource Title: Ileum_CD4Tonly. File Name: Ileum_CD4Tonly.tarResource Description: .h5seurat object of non-naive CD4 ab T cells derived from ileum samples. Untar into .h5seurat file before use.Resource Title: Ileum_gdCD8Tonly. File Name: Ileum_gdCD8Tonly.tarResource Description: .h5seurat object of gd and CD8 ab T cells derived from ileum samples. Untar into .h5seurat file before use.Resource Title: Ileum_ILConly. File Name: Ileum_ILConly.tarResource Description: .h5seurat object of innate lymphoid cells (ILCs) derived from ileum samples. Untar into .h5seurat file before use.Resource Title: Ileum_MyeloidOnly. File Name: Ileum_MyeloidOnly.tarResource Description: .h5seurat object of myeloid lineage leukocytes derived from ileum samples. Untar into .h5seurat file before use.Resource Title: Ileum_NonImmuneOnly. File Name: Ileum_NonImmuneOnly.tarResource Description: .h5seurat object of non-immune cells derived from ileum samples. Untar into .h5seurat file before use.Resource Title: Ileum_TILConly. File Name: Ileum_TILConly.tarResource Description: .h5seurat object of all T cells and innate lymphoid cells (ILCs) derived from ileum samples. Untar into .h5seurat file before use.Resource Title: PBMC_AllCells. File Name: PBMC_AllCells.tarResource Description: .h5seurat object of all cells derived from PBMC samples. Untar into .h5seurat file before use.

本数据集收录了Wiarda等人在2022年发表的预印本《通过单细胞RNA测序揭示猪小肠固有淋巴细胞及其淋巴细胞空间背景》中进行的和展示的数据分析相关文件。该研究从两只七周大的猪回肠中获取富含淋巴细胞的单细胞悬液，并对其进行单细胞RNA测序（scRNA-seq）。同时收集外周血单个核细胞（PBMCs），并行进行scRNA-seq处理。通过对淋巴细胞的转录组学分析，构建了猪小肠淋巴细胞的转录组学图谱，共注释出31,983个细胞，分为26种细胞类型。深入分析数据揭示了猪小肠中先前未描述的细胞，包括SELLhi γδ T细胞、第1组和第3组固有淋巴细胞（ILCs）以及B细胞的四个亚群。小肠中的单细胞转录组与猪血液中的转录组进行了比较，并检测到在小肠而非周围组织中存在的激活淋巴细胞亚群。与人类和小鼠小肠的scRNA-seq数据进行比较，揭示了物种间小肠淋巴细胞的普遍一致性。通过scRNA-seq前的组织差异分离，确定了猪小肠中淋巴细胞的空间背景。在带有派伊尔斑的小肠中富集了抗体分泌细胞、B细胞、滤泡CD4 αβ T细胞和循环的T/ILC细胞，而在无派伊尔斑的小肠中富集了非循环的γδ T细胞、CD8 αβ T细胞和第1组ILC细胞。数据文件包括分析论文中涉及的各个细胞亚群的.h5seurat文件。文件可用于重建不同的分析以及进行进一步的数据查询。原始数据分析的脚本可在https://github.com/USDA-FSEPRU/scRNAseq_Porcine_Ileum_PBMC找到。原始数据可在GEO访问号GSE196388中获取。数据可通过https://singlecell.broadinstitute.org/single_cell/study/SCP1921/intestinal-single-cell-atlas-reveals-novel-lymphocytes-in-pigs-with-similarities-to-human-cells在线查询。数据集中包含以下资源：

资源标题：Ileum_AllCells. 文件名：Ileum_AllCells.tar. 资源描述：来自回肠样本的所有细胞的.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：GutBlood_IntegratedILCs. 文件名：GutBlood_IntegratedILCs.tar. 资源描述：来自回肠和PBMC样本的ILCs的.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：Ileum_Bonly. 文件名：Ileum_Bonly.tar. 资源描述：来自回肠样本的B细胞和抗体分泌细胞的.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：Ileum_CD4Tonly. 文件名：Ileum_CD4Tonly.tar. 资源描述：来自回肠样本的非原性CD4 ab T细胞的.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：Ileum_gdCD8Tonly. 文件名：Ileum_gdCD8Tonly.tar. 资源描述：来自回肠样本的gd和CD8 ab T细胞的.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：Ileum_ILConly. 文件名：Ileum_ILConly.tar. 资源描述：来自回肠样本的固有淋巴细胞（ILCs）的.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：Ileum_MyeloidOnly. 文件名：Ileum_MyeloidOnly.tar. 资源描述：来自回肠样本的髓系白细胞.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：Ileum_NonImmuneOnly. 文件名：Ileum_NonImmuneOnly.tar. 资源描述：来自回肠样本的非免疫细胞的.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：Ileum_TILConly. 文件名：Ileum_TILConly.tar. 资源描述：来自回肠样本的所有T细胞和固有淋巴细胞（ILCs）的.h5seurat对象。使用前需解压缩为.h5seurat文件。

资源标题：PBMC_AllCells. 文件名：PBMC_AllCells.tar. 资源描述：来自PBMC样本的所有细胞的.h5seurat对象。使用前需解压缩为.h5seurat文件。