Which cell compartments are you interested in?
Depending on this it would be possible to give to hints.
For nuclear extraction I am using a kit from Actife Motiv which is working very fine, and they also have kits for other subcellular compartments.
Regarding mitochondria isolation I was trying with kits from Miltenyi and Qiagen, but hat in both cases problems with ER contamination...
i am looking for translocation of IKK alpha, i am working on cancer cell line LNCap
Do you have the possibility to go for Immunofluorescence staining? Seed the cells on slides and when they are 80% confluent fix them and then go for antibody / Dapi staining with and then fluorescence microscopy.
This is how I would prefer to work - first localize which compartments might be involved and then go for specific isoltation and Western blot etc. - but I think nuclei might be a good target as I would guess that it might translocate in between cytoplasm and nucleus. With the aforementioned kit from Active Motiv you would getboth the cytoplasmic as well as the nuclear fraction.
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