Partek genomics suite 6

Idiopathic PAH lung tissue and human control lung tissue were used for global profiles. The analyses for total RNA in lung tissue were performed as formerly outlined [4 (link)]. Shortly, biotinylated cRNA was prepared from 6 ug total RNA (Expression Analysis). 10 ug of cRNA was hybridized at 45C for a time period of 16 hours on GeneChip Genome Array. The data were determined with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as the normalization method. Using Partek Genomics Suite 6.6, the value definition was set up and using a t-test with a false discovery rate (FDR) of 2 fold, P<0.01 was determined. The database has been submitted to NCBI/GEO and has been approved and assigned a GEO accession number, GSE53408.

Global profiles were determined in human lung tissue and compared across normal and idiopathic pulmonary arterial hypertension patients. The total RNA lung tissue analyses were performed using Trizol extraction according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were scanned using the HuGene-1_0-st-v1 GeneArray Scanner G2500A. The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as the normalization method. The value definition was set up using Partek Genomics Suite 6.6. Significantly changed genes were determined using a minimum difference in expression of at least 200 arbitrary Affymetrix units, and P<0.01 by t-test with a false discovery rate (FDR) of 2 fold. The database has been submitted to NCBI/GEO and has been approved and assigned a GEO accession number, GSE53408.

Total RNA was extracted and reverse transcript into cDNA. Samples were then hybridized to the Affymetrix Rat Gene 1.0ST (Chengdu, Sichuan, P.R. China) in accordance with the manufacturer’s instruction. Data were normalized by Partek Genomics Suite 6.6 (Affymetrix, Beijing, P.R. China) in default analysis settings. Normalized data were processed to the Kyoto Encyclopedia of Genes and Genomes (KEGG, Chengdu, Sichuan, China) for further pathway function analysis.