For vertebrates, while most tissues are able to generate usable Hi-C libraries, brain, liver, muscle, or whole blood tend to yield the best results if available.
For invertebrates, chitinous exoskeletons or pellicles can create problems in extracting good Hi-C data. We recommend using organisms during a softer tissue stage of their lifecycle, such as larvae or pupae for insects, if possible. Using a razor blade to chop most invertebrate samples (piled into a group if using multiple individuals) is also very helpful. After crosslinking, homogenizing the tissue with a dounce or other tissue grinder leads to best release of chromatin in the following lysis steps.
Generally speaking, if you have challenges creating short-read sequencing libraries for your sample, you may experience similar challenges with Hi-C libraries as well. Any tricks you might have developed for creating short-read libraries for your sample may also be helpful; please contact us if you would like to discuss a potentially difficult sample.