Gene expression profile in the bone marrow of Ptpn6-insufficient mice with neutrophilic dermatosis-like disease (NDLD)

A total number of 1,511 probe sets in the bone marrow showed at least two-fold changes with FDR < 0.05, of which 256 probe sets had over four-fold changes. A group of 63 genes in the bone marrow of NDLD mice had more than a 4-fold change with FDR < 0.0001. From 503 genes encoding proteins with ITIM motif that binds to Ptpn6, 109 were up-regulated and 83 were down-regulated. Bone marrow samples were harvested from 5-week old homozygous Ptpn6-meb2/meb2 mice with NDLD and their wt littermates. Total RNA samples from the bone marrow and skin were isolated with Trizol (Life Technologies, Carlsbad, CA). The quality of the samples was tested with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). An Affymetrix Mouse Genome 430 2.0 GeneChip Array (Affymetrix, Santa Clara CA) was employed for the study. All labeling reactions and hybridizations were carried out according to the standard GeneChip eukaryotic 3’ target labeling protocol using the One-cycle cDNA synthesis and in vitro transcription (IVT) labeling kit (Affymetrix). Signal normalization, background correction, additional quality control and all statistical analysis were performed with the use of Affymetrix Transcriptome Analysis Console (TAC) 2.0. Robust Multi-array Average (RMA) method was used for background correction and for the normalization of hybridization signal intensities across all collected samples.