In the Agile methodology, a Story should follow the INVEST mnemonic and should aim to be as independant as possible. Now, if that is impossible, the order of the product backlog should give you the dependencies you need. If A has to be done before B, then A should be higher than B. Finally, if you really looking for a way to mark that dependency, you could use the JIRA issue link function.
...It's true that there are projects in Jira; but they are merely a way to cut off issues, to tell them apart from other sections of work and to apply rules that are specific to that team (the schemes)....
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