The first cruelty the Jews would have faced during the Holocaust was the conditions on the transports to the camps. There, they were locked into boxcars (typically) that were extremely overcrowded to the point that some people died of suffocation. These cars would have no toilet facilities and the Jews were given very little food or water (if any).
Those who were not killed immediately (in particular, those who went to concentration camps rather than killing centers) were worked extremely hard in terrible conditions. In some camps, Jews were used as subjects for medical experiments. Doctors would use them as human test animals to study things like the effects of being immersed in cold water for long periods of time.
The kinds of cruelties that were inflicted on the Jews in the camps were too numerous to list here. Please follow the links and explore the Holocaust Museum site in particular to find out much more about this topic.