There are domain-specific technical terms (verbs) to denote the actions mentioned by the OP like cleansing, scrubbing, wrangling and munging (this one is already mentioned in another answer) but I am not sure if they fit in the example sentence as it is. Perhaps it can be adapted like:
We cleansed/scrubbed/wrangled/munged the dataset of 1.5m scientific papers into a smaller one of 650k papers.
Also, distilled connotes reduction (1.5m to 650k) and improvement (processing on the table to mitigate the noises in it, handling null values, etc):
We distilled a dataset consisting of 650k papers.
: to take the most important parts of something and put them in a
different and usually improved form
He has perfectly distilled the meaning of the holiday into a poem.
A widely accepted and understood term would be prepared (as in data preparation).
We prepared a dataset consisting of 650k papers.
: to make (someone or something) ready for some activity, purpose,
: to make or create (something) so that it is ready for use
The pharmacist prepared the prescription.
Another generic(nontechnical) term would be extracted.
We extracted a dataset consisting of 650k papers.
: to get (something, such as information) from something
Investigators were able to extractuseful information from the
company's financial records.
They are hoping to extract new insights from the test results