Persistent Inflammation of the Rectum in Perianal-Fisulizing Crohn's Disease Associates with Goblet Cell Function

Leveraging single-cell RNA sequencing

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Chromium Next GEM Single Cell 3’ Reagent Kit v 3.1 Dual Index (PN-100268)

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on the 10X Genomics Chromium platform

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Assembly: GRCh38

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subject to droplet-based single-cell RNA sequencing

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6 subjects were classified as IF (5 with active fistula), 6 as non-inflamed (NI) with inactive/healed fistula

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6 subjects were classified as IF (5 with active fistula), 6 as non-inflamed (NI) with inactive/healed fistula

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and a non-inflammatory bowel disease (IBD) control was included.

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Longitudinal profiling studies are currently underway to systematically map these cellular changes

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In total, 67,119 cells from 13 individuals

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established perianal-CD patients undergoing anti-TNF therapy

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those who remain unhealed and inflamed (IF)

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Public on Feb 20 2023

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CellRanger (v.6.1.2) software was used to generate count matrices

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GSE225199_RAW.tar

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Batch effect correction was performed on the dataset

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UMAP of 15 major cell types detected by cluster analysis

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Seruat package (v.4.1.1) in Rstudio was used for quality control and clustering the data.

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rectum

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"inflammation status": {"Non-inflamed": 7, "Inflamed": 6}

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In total, 67,119 cells from 13 individuals

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"sample_count": 13

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6 subjects were classified as IF ... 6 as non-inflamed (NI) ... and a non-inflammatory bowel disease (IBD) control was included

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Rectal biopsies were processed using protease protocol.

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