Human Gut Cell Atlas (HGCA) v1 - Lymphoid Lineage

Summary

Healthy and adjacent-to-disease control data from 27 gut single-cell RNAseq datasets were collected and integrated to form v1 of the Human Gut Cell Atlas lymphoid lineage

Metadata

Dataset Type: Integrated. The file includes an integrated collection of datasets.
Total Cells: 572,267
assay: 10x 3' v3 (297,855 cells)10x 3' v2 (128,869 cells)10x 5' v1 (86,053 cells)10x 5' v2 (38,801 cells)10x 5' v3 (20,689 cells)
disease: normal (457,014 cells)Crohn disease (64,585 cells)colorectal cancer (17,156 cells)enteritis (14,511 cells)digestive system disorder (11,247 cells)polyposis (7,535 cells)adenocarcinoma (113 cells)cystic fibrosis associated meconium ileus (61 cells)necrotizing enterocolitis (45 cells)
organism: Homo sapiens
tissue: ileum (182,221 cells)jejunum (171,081 cells)colon (118,484 cells)ascending colon (38,898 cells)gastrointestinal system mesentery (26,109 cells)caecum (9,240 cells)transverse colon (8,911 cells)sigmoid colon (8,745 cells)duodenum (5,223 cells)rectum (1,537 cells)small intestine (798 cells)vermiform appendix (608 cells)descending colon (412 cells)

Cell Labels

hgca_celltype_v1

Description

Cell annotations based on two rounds of subclustering with scVI integration, sample_id as batch key. Cell annotations were refined by expert feedback based on "prelim annotation" on CAP. Prelim annotation is renamed "hgca_celltype_v0" here and the feedback on the "prelim annotation" is available by selecting a previous version of the Integrated Human Gut Atlas on CAP.

Annotation Method

both