Detailed description of the mass cytometry data set on human gastrointestinal disorders can be found in our previous work14 (link). In brief, samples (N = 102) were collected from patients who were undergoing routine diagnostic endoscopies. The cells from the epithelium and lamina propria were isolated from two or three intestinal biopsies by treatment with EDTA followed by a collagenase mix under rotation at 37 °C. We analyzed single-cell suspensions from biological samples including duodenum biopsies (N = 36), rectum biopsies (N = 13), perianal fistulas (N = 6), and PBMC from control individuals (N = 15) and from patients with inflammatory intestinal diseases (celiac disease (CeD), N = 13; RCD type II (RCDII), N = 5; enteropathy-associated T-cell lymphoma type II (EATLII), N = 1 and Crohn’s disease (Crohn), N = 10). A CyTOF panel of 32 metal isotope-tagged monoclonal antibodies was designed to obtain a global overview of the heterogeneity of the innate and adaptive immune system. Primary antibody metal-conjugates were either purchased or conjugated in-house. Procedures for mass cytometry antibody staining and data acquisition were carried out as previously described27 (link). CyTOF data were acquired and analyzed on-the-fly, using dual-count mode and noise-reduction on. All other settings were either default settings or optimized with a tuning solution. After data acquisition, the mass bead signal was used to normalize the short-term signal fluctuations with the reference EQ passport P13H2302 during the course of each experiment and the bead events were removed30 (link).
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