please refer the following link

iibce.edu.uy/NACT/Capitulo%20Tecnico%20Cremer%202008.pdf

 well, that you cannot say definately - the point is to have a protocol which in its completness is structure preserving, because each cell type has its special in and outs

nevertheless, the best protocols arround are those from the following two papers:

Light optical precision measurements of the active and inactive Prader-Willi syndrome imprinted regions in human cell nuclei.

Rauch J, Knoch TA, Solovei I, Teller K, Stein S, Buiting K, Horsthemke B, Langowski J, Cremer T, Hausmann M, Cremer C.

Differentiation. 2008 Jan;76(1):66-82. Epub 2007 Nov 26.

The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions.

Jhunjhunwala S, van Zelm MC, Peak MM, Cutchin S, Riblet R, van Dongen JJ, Grosveld FG, Knoch TA, Murre C.

Cell. 2008 Apr 18;133(2):265-79. doi: 10.1016/j.cell.2008.03.024.

unfortunately they are from work I did, but I can assure you that this protocols were first implemented in 1996/1997 and since tested dozens of times - so this is still the best around.

if you do not want denaturation, then combo-fish is the way to go, which is a variant of this protocol  - check the papers from Michael Hausmann.

a remark at the end - I have seen nearly all preparations in the last years and can tell you that there is still nothing better then the above including combo-fish = it is also interesting that many people claim doing 3D-fish with improved protocols, but you see very clearly that that are empty claims...

ah and the paper from cremer from above belongs also to our papers, actually our protocol from the above mentioned papers was developed for the project "Light optical precision measurements..." - I know, because I still have the bottle of champagne (empty of course) on my shelf when the protocol worked for the first time properly after the first preparation done by joachim rauch, irina solovei, and myself in munich...

ah and another thing, depending on what you do you also need to make the microscopy properly, because otherwise the best preparation is senseless:

therefore again the above papers and also

Super-resolution imaging reveals three-dimensional folding dynamics of the β-globin locus upon gene activation.

van de Corput MP, de Boer E, Knoch TA, van Cappellen WA, Quintanilla A, Ferrand L, Grosveld FG.

J Cell Sci. 2012 Oct 1;125(Pt 19):4630-9. doi: 10.1242/jcs.108522. Epub 2012 Jul 5.

Thank you very much, this is a well detailed helpful protocol!!

I understand that we need to improve accessibility of the probe to chromatin by multiple permeabilitizations by detergents as well as deproteinization; still may I ask about the purpose of glycerol treatment and repeated freezing thawing??

yes: the freezing and thawing is THE trick, because it breaks physically spaces, so go down with all the deproteinization stuff which chemically acts and use physical force - now does this destroy the structure: sometimes yes and you even see the breaks, on the other hand usually only the cytoplasm is affected, so not problem for the nucleus...

and be careful with the handling, the way how you treat the cells in solution or on the coverslip is important, so the real way how you pipette etc. might seem odd, but if you want a good structure preserving protocol, then take it serious out of our experience over ~20 years - and I guess you would like to deliver a proper result...

of course, I do not know what you want to show, but in terms of going to the limits of the possible I really advice you to be careful, picky, and precise at every single step down to the analysis of the microscopy...