After washing steps, following the manufacturer's instructions, the arrays were analyzed using the Agilent scanner G2505C and Feature Extraction software v.10.7.
Apoptotic cells were evaluated using the Guava Nexin Annexin V Assay kit (Millipore), following the manufacturer's instructions, and samples were analyzed using the Guava easyCyte 5HT Flow Cytometer (Millipore).
The protein expression of inflammatory cytokines and chemokines was measured by HQPLEX Analyte Kit (Mouse Inflammation 17-Plex; Cellector, San Diego, CA, USA) according to the manufacturer's instructions and data were analyzed using BeadLogic software (Inivai Technologies, Mentone, Australia).
A focused array (Lonza, Cologne, Germany; Mouse Cytokines and Receptors 00189699) was performed on colonic RNA according to the manufacturer's instructions and the results were analyzed using RealTime StatMiner software V4.0 (Integromics).
Protein bands were visualized with the use of enhanced chemiluminescence reagent (Pierce), according to the manufacturer's instructions, and band intensities were analyzed using Bandscan 5.0 (Glyko, Hayward, CA, USA).
Cells were analyzed by staining with FITC-labeled Annexin V and propidium iodide (Becton Dickinson, USA) as per manufacturer's instructions and stained cells were analyzed using a FACS Aria III (Becton Dickinson) and data were analyzed by using FlowJo software (FlowJo, Ashland, OR, USA).
Patients and blood donors from southeast France were genotyped for low resolution HLA-A, -B, -C, -DRB1 and –DQB1 loci using LABType SSO Typing Tests (ONE LAMBDA, INC , USA according to the manufacturer's instructions, and the results were analyzed using HLA Fusion v 1.2.1.
Array CGH was set up according to manufacturer's instruction and the data were analyzed using BlueFuse Multi software (Illumina) and the UCSC genome browser (http://genome.ucsc.edu).ucsc.edu
Arrays were then washed following manufacturer's instructions and the resulting images were analyzed using an Affymetrix GeneChip Scanner 3000.
Arrays were then washed as per the manufacturer's instructions and the resulting images were analyzed using an Affymetrix GeneChip Scanner 3000.
