Pooling 'very small' patient samples for ChIP Seq

[seqprone]

Hi everyone!

I've gone through a lot of threads regarding pooling of samples for sequencing. Unfortunately, I'm not confident if they address my concern.

My experiment design requires isolation of intact nuclei from patient tissues.

The isolated nuclei will then be sorted for certain markers and only the nuclei positive for target markers will be used for CHiP-Seq.

My problem is, the tissue size is about a grain of rice. The very initial hurdle is to get a good number of nuclei to begin with and then their is loss of nuclei during FACS.

Nuclei isolation improves if I start with more tissues. Can multiple patient samples from the same treatment group be processed together as the initial starting material?

I hope this question makes sense.

Would really appreciate any inputs.

Thanks!

P.s: patient's are their own control. The samples are taken before and after treatment. We're looking for changes in DNA binding site for few targets.

[shldbcrzy1]

I am also doing the same thing but with mouse tissue. Following flow i end up with small # of nuclei and would like to see what suggestions you get for your question.