Useful techniques to circumvent disruption of tissue structure in the analysis of gene expression are LCM and LDM. While they require specialized microscopes and systems, they are similar in that freshly-cut frozen tissue sections can be microdissected using either a general histological stain (like H&E) or by staining with fluorescently conjugated antibodies. The LCM system by Arcturus involves... - [Read Immunofluorescent Staining for the Laser Microdissection of Individual Cells Protocol]
Frozen tissue sections show good preservation of tissue structure and antigens. The principle disadvantages of using them in immunostaining are that the specimens must be stored frozen, and a special microtome, known as a cryostat, is required. Also, many clinical specimens are not available in this form, and most classic histological descriptions of tissue structure and pathology are based on the use of paraffin-embedded sections of formalin-fixed material. - [Read Preparing Frozen Tissue Sections for Immunostaining Protocol]
Most histological studies are carried out on paraformaldehyde-fixed, paraffin-embedded tissue samples. Therefore, there is an extensive atlas of most tissues and organs prepared from these sources, and comparing the location of antigens to these data is immediately informative. The fixation and embedding procedures are harsh, however, and many antigens are not well preserved. - [Read Preparing Paraffin Tissue Sections for Immunostaining Protocol]