Do US Universities only check your Undergrad transcripts when you?
This doesnt seem to be the case everywhere. As far as I am aware, the POI will look at your research interests, publications and whether his research area coincides with yours. Also, POI is looking for a person with a keen interest in the topic. The field in which you want to pursue further research, should coincide with your work in Masters' and also, you should score well in topics related to that field in your undergrad. To highlight the same, and make a point to the professor, I would advice you to write a SOP with relevant points mentioning your strength in his area of expertise by enunciating these points. Also, if you have some relevant reason for scoring low in certain subjects, please highlight them. It helps the POI in understanding the student and also gives your SOP a boost over others. I am doubtful if a few C's in subjects not relevant to your field of research will cast any aspersions in the mind of POI, if you are convincing. Also contact the POI before applying. Be patient.So please go ahead and apply...All the best !!! :)