Hello Anamika Chambiyal

To check the integrity of RNA, you should run RNA sample on denaturing agarose gel. Have you used denaturing agarose gel?

If you have used non-denaturing gel, then the results will be difficult to interpret because the secondary structure of RNA alters its migration pattern in non-denaturing gel so that it will not migrate according to its true size. Moreover, you will also observe multiple bands representing different structures of a single RNA species.

Please note that non-denaturing gel will not give you sharp bands as they would be seen in denaturing gel, a clear 28S and 18S rRNA bands seen for eukaryotic sample.

Please find attached below the protocol for preparing denaturing agarose gel for RNA samples, if you need one.

https://barricklab.org/twiki/bin/view/Lab/DenaturingFormaldehydeGels

Best.

You could try Dnase treatment following RNA extraction or better use RNA extraction kits from Qiagen