All viable cells (DAPI-) from Day 6 NTOC supernatant treated with: TL1A and TL1A+IL-18 were FACS-purified (Aria III, BD Biosciences) and pelleted by centrifugation at 400g for 5 mins. Cells were incubated with CD16/CD32 mAb (BD Bioscience, #553142) for 20mins at 4°C to avoid non-specific Fc receptor binding of CITE-seq antibodies, prior CITE-seq performance. Cells were washed twice with  PBS with 2% FCS used directly in downstream CITE-seq analysis. We FACS-purified 15.000 cells per sample (treatment) were loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to create single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using GemCode Single Cell 3' Gel Bead and Library kit, version 3 (NTOC supernatant) and version NextGEM 3.1 (Thymus lobes & NTOC lobes) (10x Genomics) according to the manufacturer's instructions with the addition of amplification primer (3 nM, 5'CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos. Thymic NTOC lobes were processed to single-cell suspension by pressing the organ through a 70 μm cell strainer. NTOC supernatant cells were harvested by repeated pipetting of the NTOC well and filter after the lobes were removed from the well. Samples were spun down at 400g, 4ºC for 7 min. Subsequently, samples were washed once more with 12.5 mL of cold PBS and spin down again at 400g, 4ºC for 7 min. Finally, we added 2mL of ACK lysis buffer (Westburg b.v., #10-548E) to each sample for 2 min at RT. Once incubated, we added 10mL of cold PBS to stop the lysis reaction and samples were centrifuged at 400g, 4º