Single-cell suspensions obtained from digested biopsies were stained with a Zombie Aqua Fixable Viability Kit [BioLegend] to exclude dead cells and with the following antibodies: CD20 FITC, CD8 FITC, α4[CD49d] PE [clone 9F10], CD3 PerCP, CD38 PerCP, CD4 PE-Cy7, α4[CD49d] PE-Cy7 [clone 9F10], β7 APC [clone FIB504], β1[CD29] APC-Cy7, αE[CD103] BV421, CD19 BV421 [all from Biolegend] and αE[CD103] PE (Becton Dickinson [BD]).
Fresh blood from controls [n = 20] and UC patients [n = 51] was collected into an EDTA K2 Vacutainer [BD] and immediately processed or kept in a rocking platform at 4°C [<30 min] until processing [Table S1 , Group 3]. Two hundred microlitrers of blood was incubated for 15 min with Red Blood Cell Lysis Buffer [BioLegend] and washed twice with PBS. Cells were stained with CD8 FITC, CD19 FITC, β1[CD29] PE, CD38 PerCP, α4[CD49d] PE-Cy7 [clone 9F10], β7 APC [clone FIB504], CD45RA APC-Fire750, IgD APC-Cy7, αE[CD103] BV421 [BioLegend] and CD4 PerCP [BD].
Intestinal and blood samples were fixed using BD Stabilizing Fixative [BD], and Precision Count Beads [BioLegend] were then added. Samples were acquired using a BD FACSCanto II flow cytometer [BD] and analysed with FlowJO software [BD].
Fresh blood from controls [n = 20] and UC patients [n = 51] was collected into an EDTA K2 Vacutainer [BD] and immediately processed or kept in a rocking platform at 4°C [<30 min] until processing [
Intestinal and blood samples were fixed using BD Stabilizing Fixative [BD], and Precision Count Beads [BioLegend] were then added. Samples were acquired using a BD FACSCanto II flow cytometer [BD] and analysed with FlowJO software [BD].