Q: How should I acknowledge that I have used part of my thesis for my journal article?
If I understand correctly, you want to write a manuscript which has part of your previously published PhD thesis along with some additional data that is not a part of your thesis. If your thesis is published, it is advisable to seek permission from the publisher or university who has published it before resubmitting it to a journal.
Once you have obtained permission, you can clearly mention in your cover letter of your target journal during submission that part of the study has been published as a PhD thesis and you have the approval to republish the data. You should also cite the source in your article.
This way, you can acknowledge in the cover letter that the main results for the manuscript are from your thesis and the additional experimental data that you are submitting are for comparison purposes.