Ask thesis supervisor for permission to include his name as co-author of a journal paper and risk being denied? I did my Masters Thesis at a reputed organization, under a supervisor who is an expert in the field. The organization is notoriously protective about the data I acquired from there which I need in my calculations in my thesis. I would like to publish a paper with his name too, though he had very little to do with my actual work. But I am afraid that if I ask him, he will say no, owing to the over-protective nature of the organization (though it was I who took the readings and collected the values myself). I have the option to publish it without naming my supervisor or the organization. What would be the right approach here?
It sounds like you need to consider three distinct issues:

Trade secrets / copyright: Is the data truly yours to publish? I am not a lawyer, but depending on location, type of employment and contracts / NDAs you may have signed, the simple fact that you took the readings and acquired the data might not make you legal copyright holder. What you may need - given that the organization in question is notoriously protective or even over-protective of their data - is permission to publish by the head of that institution, even if you do not intend to publish the entire data set but merely results derived from it. Formulations like notoriously protective make it seem highly advisable to look through any formal papers you may have signed prior to starting there.
Academic integrity: Even if advisors seem to have very little to do with a project, they still may have provided guidance or maybe even just the opportunity to acquire data (as in, they did the work of putting together equipment necessary to acquire the data). In those cases, it is still necessary to put the supervisor in the author list.
Affiliation: Putting the organization in the affiliations is - as far as I understand the situation - necessary, because without their equipment / setup, you could not have collected the data. Think of the CERN or DESY: Sure it's you spending the night on site when you have beam time, but you'd still put that organization in the affiliations.

I may be mistaken, but your question sounds like you feel that academic integrity warrants putting your advisor as co-author, but if you do that, people might notice that you publish work based on data acquired at that institute. And that institute might object to you publishing that data, hence you'd rather avoid &quot;waking sleeping dogs&quot;. If that's the case, i.e. if people at the institute could object to you publishing the data, you should ask before publishing.
If it turns out they'd rather not have you publish but have no legal way to keep you from publishing, there's no harm in asking and you can always publish anyways. But if they have legal means to keep you from publishing, just publishing anyways could be a very bad idea with potentially serious consequences for your reputation and your career (plus perhaps penalties to be paid, but again, I'm not a lawyer).
Email your supervisor, ask them how to proceed. It is very likely you're not the first who wishes to publish somthing based on research done there.