It'sNotMe

I am having a peculiar problem of protein of interest being detected in lysate pellet rather than supernatant after chemical lysis (M-PER Mammalian Protein Extraction Reagent). My initial thought was that the protein might have been membrane bound due to the presence binding domains at the C-terminal of the protein of interest. However, I have repeated the extraction using RIPA buffer which also resulted in protein detection in lysate pellet. Correct me if I'm wrong, eukaryotic expression does not result in inclusion bodies as prokaryotes, so it is safe to rule out aggregation and misfolding.

The following are the information of my experiment:
- Cell : CHO-S suspension cell
- Expression System: Invitrogen's Freestyle Max CHO Expression System
- Detection Method: Western Blot

Protein of Interest  Properties:
- Tags: 6Xhis and GFP
- Molecular weight: 52kDa
- Theoretical pI: 8.68
- Aliphatic index: 68.88
- Grand average of hydropathicity (GRAVY): -0.415

I am doubtful whether the protein exhibits hydrophobicity with low solubility (contrary to the hydropathicity index) or is it being precipitated by the the lysis buffer. The lysate pellet is green due to the GFP tag, which is also confirmed by fluorescence microscopy with DAPI staining. I have tried sonication with the cell being suspended in M-PER (I also suspected incomplete cell lysis). I would like to repeat sonication by using different suspension buffer i.e. PBS. In the meantime I would eagerly welcome suggestions and insights for my problem.