Yes! We encourage scientists to deposit plasmids before their paper is released, as it takes Addgene a few weeks to complete our quality control and MTA processes for all new deposits. Once you deposit your plasmids with Addgene you will acquire Addgene IDs (or URLs for kits) that you can then include in your publication. Please note you can also associate plasmids with a bioRxiv article.
If you do not want your plasmids to be available prior to your publication you can simply request that your plasmids be held offline with the Hold for Publication option during the depositing process. For more information, please see our page on depositing plasmids pre-publication. Once your paper is published you can send the Pubmed ID number to firstname.lastname@example.org and we will associate your plasmids with your publication and make the plasmids available.