As previously described(Yilmaz et al., 2012 (
link)), tissues were fixed in 10% formalin, paraffin embedded and sectioned. Antigen retrieval was performed with
Borg Decloaker RTU solution (Biocare Medical) in a pressurized
Decloaking Chamber (Biocare Medical) for 3 minutes. Antibodies used:
rat anti-BrdU (1:2000, Abcam 6326), mouse monoclonal
β-catenin (1:100, BD Biosciences 610154), rabbit monoclonal OLFM4 (1:10,000, gift from CST, clone PP7),
rat anti-CD3 (1:200, eBioscience, clone 145–2C11), rat anti-CD4, (1:200, Biolegend, clone H129.19),
rat anti-CD8 (1:200, Biolegend, clone 53–6.7),
anti-Ki67 (1:200, Thermo Fisher, MA5–14520).
Biotin-conjugated secondary donkey anti-rabbit or anti-rat antibodies were used from Jackson ImmunoResearch. The
Vectastain Elite ABC immunoperoxidase detection kit (Vector Labs) followed by
Dako Liquid DAB+ Substrate (Dako) was used for visualization. All antibody incubations involving tissue or sorted cells were performed with Common Antibody Diluent (Cell Signaling).
Beyaz S., Chung C., Mou H., Bauer-Rowe K.E., Xifaras M.E., Ergin I., Dohnalova L., Biton M., Shekhar K., Eskiocak O., Papciak K., Ozler K., Almeqdadi M., Yueh B., Fein M., Annamalai D., Valle-Encinas E., Erdemir A., Dogum K., Shah V., Alici-Garipcan A., Meyer H.V., Özata D.M., Elinav E., Kucukural A., Kumar P., McAleer J.P., Fox J.G., Thaiss C.A., Regev A., Roper J., Orkin S.H, & Yilmaz Ö.H. (2021). Dietary suppression of MHC-II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell stem cell, 28(11), 1922-1935.e5.