Sample Methods Paragraph for Use in Publications

Below are sample paragraphs you might use in publications, posters and manuscripts (Materials and Methods Sections).

Please ask TACMASS for specific conditions for your project. Mix and match, and edit as needed. 

Remember to Cite Use of TACMASS Services in manuscripts and abstracts.

Make a block and H&Es:

Tissue was harvested, fixed in 10% neutral buffered formalin for 24 hours, processed and embedded into paraffin blocks. Routine Hematoxylin and Eosin (H&E) stains were performed on 3μ sections of tissue cut from the formalin fixed, paraffin embedded (FFPE) blocks.

Make a cell line block and H&Es:

Cultured MCF-7 cells were trypsinized, washed in PBS and fixed in 10% Neutral Buffered Formalin for 24 hours. Cells were processed and embedded into paraffin block (ThermoShandon Cytoblock kit #7401150). Formalin fixed, paraffin embedded (FFPE) tissue blocks were sectioned at 3μ, baked for one hour at 60°C and stained for routine Hematoxylin and Eosin staining (H&E), or immunohistochemistry (IHC).


Immunohistochemistry (IHC) was performed on the VMSI Discovery XT Automated Immunostainer (Ventana Medical Systems, Inc, Tucson, Arizona). All steps were performed on this staining platform using VMSI validated reagents, including deparaffinization, antigen retrieval (cell conditioning), and antibody incubation and detection. Cell conditioning was performed using a borate-EDTA buffer (CC1) for 30 minutes at 100°C.

The primary antibody assay was validated (optimized) to identify optimal conditions for cell conditioning, dilution, incubaton and detection for each antibody. Localization of the primary antibody was accomplished using an appropriate biotinylated secondary antibody followed by incuation with streptavidin-HRP and DAB (diaminobenzidine) system. Following online counterstaining with hematoxylin, slides were dehydrated offline through graded alcohols to xylene and coverslipped with mounting medium (Richard Allan #4112).

A section of control tissue was placed onto each experimental slide as a positive assay control.
A positive assay control tissue was stained with each experimental run on the instrument.


Images were captured using an Olympus BX50 and CellSens DP72 Imaging system (this is the microscope and camera in the lab) or Paxcam 3 camera with PAX-it Digital Image Management & Image Analysis (this is the camera in Dr. Nagle’s office). Images were standardized for light intensity. No automated analysis of the data was performed. 

Long Score = % of cells positive multiplied by intensity @ neg, trace,1+,2+,3+,4+. Long scores for both cytoplasmic and nuclear can be generated as needed.