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Thank you for sharing your experience, and congratulations on your acceptance! I was just curious to know if your research mentor(s) and prospective faculty asked about your low undergraduate GPA? If so, how did you approach talking about this topic?
I like to think that your research mentors are truly there to help you and inevitably, to write you a strong letter of recommendation unless they say they don't know you well enough to provide that. I would try to have these conversations soon, in case someone on your list cannot provide you with a letter of recommendation. I'm primarily interested in cellular and molecular neuroscience with a focus in neurodegenerative diseases, and I've found a few mentors at Baylor, UT: Houston, Texas A&M, University of Utah, University of Iowa, and Tulane with research interests that mesh really well with mine!
Thank you for posting this! I am also hoping to enter a neuroscience PhD program fall of 2018. I have already started to freak out about the application process, but remember: everything you have done has led you up to this! Have you had a chance to talk to your research mentor(s) regarding your graduate school plans, and whether or not they'd be open to writing you a strong and favorable letter of recommendation? While it can be hard to kick the feeling of poor grades, try to focus on the things you can change on your application. In your case, I'd say you have strengthened your application by working as a research assistant and by obtaining your Master's. Oftentimes, less than stellar grades can be outweighed by stronger GRE scores, letters of recommendation, research experience, and your personal statement. I hope this helps!