I am a PhD student -- my usual stipend via W-2 (low tax) was given as a 1099-MISC this year, how can I lower my tremendous tax rate?

I am a PhD student and usually get my teaching and research stipend through my university, in the form of a W-2. In 2019, I received BOTH a W-2 and a 1099-MISC. This is because my professor I work with left for another university halfway through, and so he paid me from the other university, I received a 1099-MISC for this.

 

I just inputted everything and say the high 15.3% tax rate I was given for the funds he gave me through the other university. My usual tax rate is much lower if I were to report it all on a W-2

 

At this point, because my tasks in the W-2 and 1099-MISC are essentially the same (research and teaching), is there a way I can lower my tax rate on the 1099-MISC?

 

A KEY point was that I was hired by his new university as an "independent contractor" doing research. In fact, they even made me sign a contract stating I was an independent contractor. This might have been for convenience. The reality was that I was a PhD student receiving a stipend for research performed. The total difference in taxes I am facing is around $4,200. Thank you for any help!