mTEClo/int RNAseq profiling in three mouse models of impaired mTEC/Tcell crosstalk

mTEC/Tcell crosstalk drives transcriptional and epigenetic programs conditioning immunological tolerance Total RNA was isolated with miRNeasy Micro Kit (Qiagen) from mTEClo/int cells (EpCAM+ UEA-1+ Ly51lo CD80lo/int) from individual mice of three different mouse models in which the mTEC/Tcell crosstalk is impaired: CIITA-KO [CIIta(III+IV)-/-] vs WT ; K14xCIITAKO vs WT and RipmOVAxOTII vs OTII. The extracted RNA was used to generate transcriptome libraries using the SMART-Seq-v4-Ultra Low Input RNA Kit (Clontech) combined to the Nextera library preparation kit (Illumina) following the manufacturer's protocols. Single-end (75 bp) sequencing was performed using the Illumina NextSeq 500 machine.