After constructing a metastatic cancer model, I would like to look at autophagy markers in C57BL/6 type mice. Which method should I choose other than WB and IHC?
As I have understood, you already have the tissue lysate so you do not have a reach to other markers such others suggested (autophagy bodies, cDNA ..).
If this is the case you may try a proper type of chromatography, you can also check the following link:
Muratore KA, Grundhofer HM, Arriaga EA. Capillary Electrophoresis with Laser-Induced Fluorescent Detection of Immunolabeled Individual Autophagy Organelles Isolated from Liver Tissue. Anal Chem. 2016 Dec 6;88(23):11691-11698. doi: 10.1021/acs.analchem.6b03270. Epub 2016 Nov 9. PMID: 27783895; PMCID: PMC5301951.