As mentioned by yanks1ny , TPX tubes improve significantly the shearing. For chromatin shearing, always use High Power. Using the cooling system from Diagenode instead of ice could help with consistency and reproducibility. Do you performed the reverse of cross-linking ( the pictures look like no de-crosslinking were perform)? The fixation may also affect the shearing efficiency. The best way is to trypsinize the cell and fix them in suspension in PBS but on directly on dishes. Fixing of dishes might results in the formation of cell aggregates which are difficult to disrupt. You can find a lot of tips on chromatin shearing with the Bioruptor at http://www.diagenode.com/media/documents/downloads/protocols/The_Ultimate_Guide_for_Chromatin_Shearing_Optimization_with_Bioruptor_protocol.pdf.
I don’t know why Joe_263 wants to perform ChIP on a high number of cells. Probably because Joe_263 wants to study Transcription factor. So, the answer of KPDE is good. Joe_263 has to optimize the shearing with lower concentration of SDS. Diagenode has a “chromatin shearing optimization kit with low SDS” and can help this customer by E-mail (techsupport@diagenode.com or techsupport.na@diagenode.com ).
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