Foxp3 fix perm concentrate and diluent kit

FACS analysis was undertaken as described previously (Mattarollo et al., 2010a) . Foxp3 Fix/Perm Concentrate and Diluent kit was used for intracellular staining (eBioscience, San Diego, CA). CXCL9 and CXCL10 were stained intracellularly with unconjugated goat anti-mouse polyclonal antibody (R&D Systems, Minneapolis, MN) followed by phycoerythrin-conjugated secondary donkey anti-goat IgG H&L antibody (Abcam, Cambridge, UK). Anti-mouse monoclonal antibodies to CD45.2 (104), CD45.1 (30-F11), CD8a (53-6.7), TCRb (H57-597), CD11b (M1/70), EpCAM (G8.8), CD19 RNA extraction, reverse transcription and quantitative PCR RNA Extraction was performed as described (Zhussupbekova et al., 2016) . For each reverse transcription, 1 mg of extracted RNA was processed using a SuperScriptIII kit (Life Technology, Beverly, MA). Primers sequences can be found in Supplementary Table S2 online.
Quantitative PCR was carried out on Applied Biosystems Quant-Studio 6 Flex Real-Time PCR System (Applied Biosystems, Carlsbad, CA).
Sequencing and analysis, Gene Set Enrichment Analysis, and Gene Ontology Analysis RNA sequencing and raw data processing were done as described previously (Zhussupbekova et al., 2016) . Detailed methods for Gene Set Enrichment Analysis and Gene Ontology Analysis can be found in the Supplementary Materials and Methods online.