MyEntity e = new MyEntity();

// scenario 1
// tran starts
em.persist(e);
e.setSomeField(someValue);
// tran ends, and the row for someField is updated in the database

// scenario 2
// tran starts
e = new MyEntity();
em.merge(e);
e.setSomeField(anotherValue);
// tran ends but the row for someField is not updated in the database (you made the changes *after* merging

// scenario 3
// tran starts
e = new MyEntity();
MyEntity e2 = em.merge(e);
e2.setSomeField(anotherValue);
// tran ends and the row for someField is updated (the changes were made to e2, not e)