To add to the great answer by Buffy, PhD applications are considered on multiple factors, and the school the candidate went to, is just one of them. As mentioned above, you have a master's school to balance out with undergraduate school. I think you have done the right thing by adding research experience and other skills to your resume and that will be considered favorably too.
Also, something to ask yourself is what you want out of the grad school - do you want your own research lab in a university or are you looking to pursue research in industry? At least in the USA, getting into academia is hard because an unfair amount of weight is given to the university where one gets their PhD. If you are reasonably certain or open to considering industry positions, it does not matter if you went to a top grad school and instead more weight is given to the quality of your work.
Finally, for the statement letter and all interviews going forward, I recommend identifying your story and then drawing relevant pieces from all your experiences to match the narrative of your story. As long as you can identify what you learned and gained from your undergraduate and master's schools and tie them to your story, you can highlight them as your strengths instead of something that holds you back. Good luck!