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I am designing a device that will have Gigabit Ethernet ports on it. We have a requirement that our device must be stored at -50C. Many gigabit ethernet transformers either don't list a min storage temperature in the datasheet, or the min is -40C.

I found some non-PoE type gigabit ethernet transformers that supported storage temperatures down to -50C, but they were sort of expensive. One example being the Pulse HX5008FNL (like $6~$7 at quantity = 100).
https://www.mouser.com/datasheet/2/336/-595196.pdf

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I also found some PoE type gigabit Ethernet transformers that supported storage down to -50C, and they were much cheaper. One example being the Bourns SM51625EL (like $1.50 at quantity = 100).
https://www.mouser.com/datasheet/2/54/sm51625el-934089.pdf

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From the datasheets, both parts seem to have similar common mode rejection, insertion loss, cross talk, etc.

My device will not be implementing PoE, just regular gigabit data transfer, and I wont have the power supply controller that normally goes with a PoE transformer. But I want to use the cheaper part...

I know you can't use a non-PoE transformer for PoE, since they are not designed to handle larger currents. But is there any downside to using a PoE type transformer in a non-PoE application.

Also, I am using the VSC8541-2 Ethernet PHY. Page 25 of the datasheet shows that (if I wanted to) the chip can be used in PoE applications (with a separate PoE power supply).
https://ww1.microchip.com/downloads/en/DeviceDoc/VMDS-10513_VSC8541-02_VSC8541-05_Datasheet.pdf

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Can you use it? Yes you can.

Raspberry pi uses a PoE transfromer but doesn't support POE (an additional circuit can be added to provide POE)

I'm not aware of any major downsides.

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