Differential input conversion using Arduino Uno

hi
i need perform a/d conversion differential signal using arduino uno. have tried software method connect 1 i/p a0 , a1, read adc both channels , subtract in code. 100 ms time convert analog signals causing errors not differential signal conversion(ie there delay between 2 samples taken , hence not differential signal.)

now not sure this, can connect 1 of analog inputs arduino uno gnd pin , perform conversion other signal ie 1 i/p ground of arduino a0 of arduino , perform a/d conversion a0. correct? cause damage circuit perspective? there other metod without using external differntial adc?

regards

dpk

if 2 systems not connected (e.g. common power ground) ok connect 1 of analog outputs arduino gnd. 
!!!!! signal going analog input must never go negative, (see datasheet)
a diode may safeguard. refer components datasheet find if output may shortcircuit proof

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