mTECs were sorted based on the following markers: DAPI-, CD11c-, CD45-, Ly51-, EPCAM+, Class II+. RNA was isolated using Qiagen’s RNeasy Micro Plus Kit and amplified using Sigma Whole transcriptome amplification kits.
Label
Cy3-CTP
Label protocol
Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc, Madison, WI)
Hybridization protocol
Labeled Cy3-cDNA was assesed using the Nanodrop ND-8000 (nanodrop Technologies, INC, Wilmington DE), and equal amounts of Cy3 labeled target were hybridized for 17hrs to Agilent whole mouse genome 4x44K ink-jet arrays.
Scan protocol
Arrays were scanned using the Agilent microarray scanner.
Data processing
Raw Signal intensities were extracted with Feature Extraction v10.6 software.
