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He had displayed the flag in a flower pot at Saticoy Elementary School and, on 22 May, found it burned and the pot broken.
The incident is being investigated by Los Angeles police as a possible hate crime.
“We experienced a break-in over the weekend at Saticoy Elementary that resulted in vandalism and is being investigated as a hate-motivated incident,” the school told parents in a statement.
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“We are cooperating with law enforcement. This is a reminder that we rely on our entire school community to keep our school safe and secure by reporting any suspicious activity on campus after hours. If you see something, say something.”
The teacher initially remained at the school, though the Los Angeles Unified School District has since removed him due to concerns for his safety, according to the Los Angeles Times.
Saticoy Elementary School has seen protests from conservative parents in recent months, with a group of them creating an Instagram account on 16 May in protest of its Pride Month assembly which planned to teach students about families with same-sex parents.
Some expressed their fury over “sexuality” being taught in schools, while others vowed to keep their children home.
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The account has been used to post photos of the teacher, whose image has been taken down from the school’s website, both before and after his transition.
Speaking to the Los Angeles Times, a teacher at Saticoy Elementary School, who requested anonymity, said: “We’re in an atmosphere especially here in the United States with school shootings where, no, I don’t feel safe.
“I don’t think any of our teachers feel safe. And a lot of parents don’t feel safe about their children either.”