Chromatin immunoprecipitation was done as described in http://labs.fhcrc.org/hahn/Methods/mol_bio_meth/hahnlab_ChIP_method.html [ http://mcb.asm.org/content/31/4/818.long ] with the following modifications. Briefly, 100 ml cell cultures were grown to an A600 of 0.8 to 1 in YPD medium at 30°C. Cells were lysed in ChIP lysis buffer in the presence of 0.5 mm glass beads (BioSpec Products Inc.) for 4 x 5 min with 2 min pauses in between in a Vortex Genie 2 at speed setting of 10 in multiple 1.5 ml microfuge tubes. Shearing of chromatin was done in an E220 Focused-ultrasonicator [Covaris] under following conditions: Peak Incident Power (W): 175; Duty Factor: 10%; Cycles per burst: 200; Treatment Time: 420 sec; Temperature: 7oC; Sample volume: 130 ml. An AFA Fiber Pre-Slit Snap-Cap [6 x 15mm] microTUBE [Covaris] was used for the shearing. For immunoprecipitation, 2mg of TAP polyclonal antibody (Thermo Scientific; Product # CAB1001; Lot # NH77071) or CgPdr1 specific polyclonal antibody (described above) was used. The library preparation of ChIP-ed DNA was done on the Nugen Mondrian SP Workstation: http://www.nugen.com/nugen/index.cfm/products/msp/products/workstation-plus/ with the Ovation SP Ultralow DR Multiplex System: http://www.nugen.com/nugen/index.cfm/products/msp/products/ultralow/
GEO Accession
GSM1447362