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In his resignation letter to Governor Arif Mohammed Khan, who is also the chancellor of universities, Dr Saseendran stated he was stepping down due to personal reasons.
The college was shut down following the death of Sidharthan JS, a second-year student of the veterinary varsity.
The decision comes in the wake of protests by student organisations and various pending probes in the case.
Son of a popular Congress leader in Wayanad district is also booked in the case.
Alleging lapses in the police investigation, Congress demands a CBI probe into the case.
It is learnt that the minister took action against the officials amid mounting political pressure.
Order from CM's office on Thursday to constitute a Special Investigation Team had signalled the police to speed up the arrests.
He claimed that he had directed a senior student to inform Sidharthan's family within 10 minutes after finding him hanged in the hostel toilet.
Sinjo's arrest made headlines hours after the probe team issued a lookout circular (LOC) against four absconding accused in the case.
He received the suspension order through WhatsApp amid preparations to suspend the college Dean and assistant warden of the men's hostel.