and stained with antibodies for cell surface markers. The following antibodies were used
for FTOC samples: CD5-FITC (clone 53-7.3) and CD44-PE-Cy7 (clone IM7) from BD Biosciences;
TCRβ-APC (clone H57–597), CD24-Pacific Blue (clone M1/69), and
TCRγδ-PerCPCy5.5 (clone GL3) from BioLegend; CD25-PE (clone PC61.5) and
CD8α-APC-eFluor780 (clone 53-6.7) from eBioscience, and CD4-Qdot605 (clone RM4.5)
from Life Technologies. The following antibodies were used for thymic slice samples:
CD45.1-FITC (clone A20), CD69-PerCPCy5.5 (clone H1.2F3), CD5-PE (clone 53-7.3), CD4-PE-Cy7
(clone RM4–5), CD8α-eFluor450 (clone 53-6.7) from eBioscience. For
negative selection experiments, cells were pre-stained with LIVE/DEAD Fixable Aqua Dead
Cell Stain kit (Molecular Probes) for thirty minutes in PBS. Data were acquired on an
LSRII or LSR Fortessa (BD Biosciences) and analyzed using FlowJo software (Tree Star).