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I am reading the datasheet of PoE Magnetics. I am not able to understand which side belongs to cable side and which belongs to ethernet controller.

Is it possible to use any of the side for ethernet controller? I have read this documents and it says:

The 8-core magnetic only has a transformer and a CMC. The CMC construction and purpose is the same as 12-core magnetics, but the CMC can be located on either the cable side or the PHY side of the transformer. Based on PMA compliance testing results when transformers have CMC on the PHY side, it is recommended that future designs avoid this magnetic configuration. The template test for PMA compliance has reduced margin in the PHY-side CMC location compared to the cable-side CMC.

It looks like Common mode choke should be facing the cable side (away from Ethernet controller). Is it correct statement?

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In its datasheets, e.g. this, Pulse Electronics typically labels the chip side circuits with D letter while it labels the medium side circuits with X letter: TD+ <-> TX+, TD- <-> RX-, ect...

Therefore, pins 1,2,3,6,7,8 of an H(X)2260NL transformer are (nominally) chip side pins. If you need an oppositely crossed one, have a look on H(X)1260NL.

It looks like Common mode choke should be facing the cable side (away from Ethernet controller). Is it correct statement?

It is application dependent. No single method exists. In your case, Pulse's PoE-enabled transformers H(X)2260NL and H(X)2305NL implement CMCs at the chip side.

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