Hlo dear,
I would suggest you to take CSE.
As far as I have noted that CSE students get to learn core computer science papers while IT more of general stuffs. They never had Detailed Algorithms or theory of computation which are of more importance in GATE or related exams.
Some companies specifically wanted only CSE dept students to attend the interview despite the fact that IT is quite similar to CSE. So it's better to choose CSE.
Thank you.
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