According to the PCIe standard the PERST# signal (reset-gpio in fsl,imx* compatible dts) should be kept asserted for at least 100 usec before the PCIe refclock is stable, should be kept asserted for at least 100 msec after the power rails are stable and the host should wait at least 100 msec after it is de-asserted before accessing the configuration space of any attached device.