Using low pass filter for a differential ended receiver system?
If the source is diff ended and the data acq. is also diff ended?


If the DAQ input is differential then you need to attenuate the differential signal at higher frequencies so, use resistors in series with each input and a capacitor directly across the DAQ input after the resistors.


  If the source is single ended and the data acq. is diff ended?


You do exactly the same because you don't want to imbalance the impedance of lines that could pick up external inteference (common-mode) and, due to those impedance imbalances, convert a common mode interference to a differential interference.



You might also need to consider impedance balancing at the source and cabling between source and DAQ. You might also need common mode decoupling capacitors to help reduce noise. This is for noise reduction rather than anti-alias filtering.