miR-17 seed family specific targets in two Hodgkin lymphoma cell lines

The aim of the study is to identify miRNA specific targets in Hodgkin lymphoma cell lines. By immunoprecipitation (IP) of wild type Ago2, Ago2 associated gene transcripts (ie miRNA targets) are coimmunoprecipitated. In cells transfected with anti-miR-17/20/93/106, the miR-17 seed family specific targets are not coimmunoprecipitated with Ago2. With microarray analysis, signal intensities of probes associated with Ago2 from untransfected and anti-miRNA transfected cells are compared. Gene transcripts that are depleted from the Ago2-IP fraction upon miRNA inhibition (ie miRNA specific targets) are identified. RNA isolated from the Ago2 immunoprecipitated (IP) fraction is hybridized against the RNA from total cell lysate (T) fraction. The experiment is performed in two independent Hodgkin lymphoma cell lines, L1236 and L428. Samples included anti-miR-220 transfected L428, anti-miR-17/20/93/106 transfected L428 and anti-miR-17/20/93/106 transfected L1236. All hybridizations are performed with a dye swap design.