ID_REF = VALUE = RMA signal intensity Log2
The data were analyzed with Robust Multi-array Average (RMA) using Affymetrix default analysis settings. All normalized RMA intensities (Log2)that were below 6.5 were set as 6.5.
Scanned using Affymetrix GeneChip Scanner 3000.
Followed Affymetrix instructions.
The samples were crushed using a sterile 16 G needle in tubes on dry ice. In the case of the intestine, the sample was resuspended in TRizol and extruded through a 16 G needle using a syringe and RNA was isolated according to manufacturer's protocol; for the Peyer's patch, the sample was suspended in cell lysis buffer and RNA isolated using the RNeasey kit (Invitrogen) according to the manufacter's protocol.
C57BL/6 female mice were orally gavaged with 1000 cysts and on Day 5 individual Peyer's patches and small intestines were dissected and analyzed for parasite burden by bioluminescence imaging. Individual Peyer's patches and intestinal sections (with the Peyer's patches removed), corresponding to the middle third of the intestine (~jejuem), that had equivalent parasite burden were snap frozen in liquid nitrogen.
Tissue cysts were obtained from the brains of chronically infected C57BL/6 mice, enumerated and resuspended in PBS at a concentraion of 1000 cysts per 200 ul PBS.