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ChIP-MS (SICAP Priority 2-3 (understand each step of the protocol, apply…

- - - - cell type (K562 vs HeLa)
      - Ab issue?
      - locus issue?
      - pA vs pG
    - - Additional check (QC) of samples prior MS
        
        systematic check and comparison of protein/DNA amount prior IP, after IP and after iST
        
        WB
        
        PAGE or/and BA, prior iST?
        
        qPCR/DNA yeild
      - masking the specific signal by Ab ?
      - Himanshu vs Pinar workflow
        
        cell type
        
        Chromatin prep (frozen vs fresh, Fixation, amount of proteins/DNA per IP etc)?
        
        speed vac
        
        de-cross-linking
        
        washes
        
        Ab batch?