I am a F-1 student since Dec 2003. All these years I used our university software to file 1040NR-EZ tax form and get refund because of the US-China (PRC) $5000 treaty. This year I can not use it anymore as my status becomes tax resident. Which form should i file if my only income is from the university paying for my RA? and can i still claim for the treaty? I would greatly appreciate your answers.

On the resident tax return you get standard deduction of $5,450. You do not get treaty deduction and must pay SS tax and Medicare tax.

Actually, under an exception to the Savings Clause in the U.S.-China Tax Treaty, the OP CAN claim the $5,000 treaty exemption as a negative number on Line #21 of Form 1040.