For up-regulated genes all of the GO processes identified by microarray profiling are also present in the RNA-seq data set; some additional categories were identified in the RNA-seq profile only, including fatty acid oxidation and glucose transport (Additional file 11A).
The up-regulated or down-regulated changes in gene expression following GANT61 treatment and determined by cDNA microarray profiling, were confirmed by qRT-PCR (Figure 5).
Comparative genomic hybridization followed by mutational analysis, gene expression and miRNA microarray profiling were performed on 123 paired tumor and non-tumor tissue samples from patients with NSCLC.
A list of targets, along with their description, is given in Additional file 7. The miRNAs found to be up-regulated by hypoxia (based on deep sequencing or microarray profiling) were searched for the presence of HREs within the promoter region (within 5 kb upstream of the 5′ends of pre miRNAs).
Up-regulation of stress response (MAFK, IKBZ, SOCS3) and early growth response (c-Myc, c-Jun, c-Fos, DUSP1 and 6) genes as assessed by RT-qPCR and/or microarray profiling was unchanged.
A comparative analysis of v-Src regulated mRNA species examined by northern blotting and microarray profiling was performed for all mRNA species included in Figure 3.
Microarray profiling was performed by Cogenics (Morrisville, NC).
Genome wide microRNA microarray profiling was performed by using a microRNA biochip platform (Febit, Heidelberg, Germany).
As expected, the fraction appearing to contradict the results of GeneChip microarray profiling is diminished somewhat by subtracting out the 408 genes that appeared in both of the two reciprocally subtracted libraries H56 and H57.
