miRNA analysis in myofibroblasts derived from normal oesophagus and esophageal cancers

We prepared miRNA from myofibroblats derived from normal oesophagus and esophageal cancers. miRCURYTM LNA Array ver5 was performed and comparisons were made by the dual (reference) method. Briefly, we have myofibroblast (NTM) from normal stomach and oesophagus, and we would like to establish whether there is tissue specific myofibroblast miRNA signature. Within the stomach (gastric) we made myofibroblasts from cancer (CAM) and adjacent tissue (ATM) from the same patients and myofibroblasts from healthy individuals (NTM) and we want to compare the matching ones paired and the total numbers unpaired. We have the same experimental design within the oesophagus but there we have two types of cancers (squamous and adenocarcinoma) so we wanted to do them separately for the two different groups and all together. In order to facilitate comparisons within each tissue type, we have used a different common reference for each tissue, and to compare between tissues using single colour analysis. Dual reference method was used to compare samples within a tissue and singe channel (quantile method) was used to compare samples across tissues.