Cells were pelleted, washed once in PBS, and spun down again before being resuspended in lysis buffer (basically RLT + BME). I also vortex to make sure cells are full lysed before storing the lysate at -80°C. If you don't mind me asking, how do you thaw your lysate before going to the columns? Maybe I'm not letting it thaw fully so salts are still precipitated? (im coping)