Some universities accept only university transcripts; others accept college transcripts or even an attested mark sheet. Some universities require you to submit 2 transcripts. It is very important that you read the American university requirements carefully before applying. Make sure you do not send them the wrong document type as it will delay the admission process.
These are issued by the university your college is affiliated to e.g. M.I.T. College in Pune is affiliated to Pune University. If you are a student of that college and the American university you are applying to requires university transcripts, you should get transcripts from Pune University.