Differential effects of tofacitinib on macrophage activation contribute to lack of response in ulcerative colitis patients

Cell suspensions were processed using the 10x Genomics 3' mRNA single-cell method

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Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

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loaded onto the Chromium10x Genomics platform

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Gencode release 27, assembly GRCh38 p10

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Single-cell RNA sequencing of intestinal cells

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Adult

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Colon biopsies from patients with active UC starting tofacitinib

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Timepoint/visit characteristics vary within subjects

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11 distinct subject/participant IDs across GEO samples

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GEO sample characteristics document treatment/therapy

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Response was defined as a decrease in the endoscopic Mayo score of at least 1 point from baseline

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We generated scRNA-seq data ( Figure 1C ) from 23 colonic samples (taken at baseline and during follow-up) from a subset of patients ( n = 11) in the Barcelona cohort

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The analysis code can be found at our GitHub website

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"isOpenAccess": "Y"

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"patient": "TOF_005"

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matrix.mtx.gz

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Supplementary files format and content: Tab-separated values files and matrix files

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GSE253006_RAW.tar

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To correct batch effects across samples, we applied Harmony

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The annotation of each subcluster ... was defined by the marker genes, which were obtained by the FindAllMarkers function

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doublets were assessed using the scDblFinder R package

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We then logarithmically normalized them

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we filtered the low-quality cells based on the mitochondrial RNA percentage and the number of genes per cell

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"tissue": {"Sigma": 14, "Rectum": 8, "Descending colon": 1}

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patients with active UC

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A total of 69,813 high-quality single cells were considered for the analysis.

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Colon biopsies from patients with active UC starting tofacitinib were collected at baseline (n=11) and during follow-up (n=12) and processed by scRNA-seq.

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"patient": "TOF_005"

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Endoscopic colonic biopsies (4-8 from each patient) were collected

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