Hi all,

I am writing to request technical suggestions for improving chromatin fixation conditions in PBMC samples for Hi-C assays. Here is my current experimental context:

Experimental Workflow:

I also tried RBC lysis directly to collect the cells as DOVETAIL protocol, but no significant improvement was observed.

I am wodering

• Would increasing FA concentration (e.g., to 3%) enhance nuclear crosslinking efficiency while maintaining chromatin accessibility for restriction enzymes?
• Could paraformaldehyde (PFA) provide better preservation of 3D chromatin structure compared to FA in this context?
• Or any other recommendations to improve the sample processing to achieve better cis/trans ratio?

I would greatly appreciate any insights or literature references regarding PBMC handling and chromatin stabilization for 3D genomics.

Best,

Junfeng