Single cell sequencing data on ileum and mesentery tissue from Crohn's disease patients

For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5′ Kit v.2 was used for mouse cells and Chromium Single Cell 5′ Library Kit was used for human cells

Section Methods—Single-cell RNA profiling, offset —

Chromium Single Cell 5' Library Kit was used for human cells

Section Methods; Single-cell RNA profiling, offset —

For sample preparation on the 10x Genomics platform

Section Methods—Single-cell RNA profiling, offset —

Assembly: GRCh38-2020-A for 5' RNA expression

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Single cell RNA sequencing (scRNA-seq) of sorted live, CD45 + mesenteric cells

Section Results, offset —

Single cell RNA sequencing (scRNA-seq) of sorted live, CD45 + mesenteric cells from 3 CD patients with matched mesentery draining from inflamed and non-inflamed regions of the ileum.

Section Results, offset —

paired inflamed ileal-draining mesentery surgical samples and non-inflamed ileal-draining mesentery surgical samples

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Control (Gastrointestinal cancer)

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We used single cell RNA sequencing to compare the immune cells in paired inflamed ileal-draining mesentery surgical samples and non-inflamed ileal-draining mesentery surgical samples

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Ileum and the associated mesentery was also collected from gastrointestinal cancer patients

Section samples, offset —

Customized code for both analysis of the scRNA-seq data and generation of some of the figures is available via GitHub

Section Code availability, offset —

De-identified human scRNA-seq data analyzed in this study are publicly available in the Gene Expression Omnibus (GEO) database ( GSE255722 ).

Section Data availability, offset —

Excel sheet showing the age, sex and tissue type obtained from patients for human experiments.

Section Supplementary information, offset —

RNA_matrix.mtx.gz

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Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data

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GSE255722_RAW.tar

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Cells expressing LTA included naive B cells, memory B cells, plasma cells, several subpopulations of memory T cells and some plasmacytoid dendritic cells.

Section Results—Contrasting roles of LTα3 and TNF in sustaining B cells in ileitis, offset —

scDblFinder 64 (v.1.2.0)

Section Methods—Software, offset —

Dead cells were excluded using a Live/Dead Aqua Fixable Cell Stain Kit

Section Methods—Flow cytometry, offset —

Ileum and the attached mesentery was collected

Section series_overall_design, offset —

paired inflamed ileal-draining mesentery surgical samples and non-inflamed ileal-draining mesentery surgical samples

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"library_strategy": {"OTHER": 24, "RNA-Seq": 13}

Section sample_values_with_sample_counts, offset —

from 3 CD patients with matched mesentery draining from inflamed and non-inflamed regions of the ileum

Section Results—Contrasting roles of LTα3 and TNF in sustaining B cells in ileitis, offset —

Discarded human mesentery tissues came from patients with CD that were undergoing bowel resections at Washington University School of Medicine.

Section Methods—Patient samples, offset —