I have tried with ultracentrifugation, but the isolation is not giving me good results with WB. I have included step for percol removal, but i think there is contamination of golgi and ER fraction
there is a method for harvesting complete endomembranes without an ultracentrifuge (http://www.ncbi.nlm.nih.gov/pubmed/20193653), but in this version you will surely get ER and golgi in your prep. The idea here is using a high density buffer which is altered during the fractionation to gain a better yield and purity of the fractions by differential sedimentation. You might try to modify the protocol, maybe you can get a better purity.