Yes, cDNA produced at the end of the Click-iT Nascent RNA Capture Kit, for gene expression analysis (Cat. No. C10365) workflow (step 6.8 on page 11 of the Manual) can be used for next-generation sequencing (NGS) application.
Below are some references of the downstream NGS application using this kit:
Palozola, K. C., Donahue, G., & Zaret, K. S. (2021). EU-RNA-seq for in vivo labeling and high throughput sequencing of nascent transcripts. STAR protocols, 2(3), 100651.
Lu, X. M., Batugedara, G., Lee, M., Prudhomme, J., Bunnik, E. M., & Le Roch, K. G. (2017). Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic acids research, 45(13), 7825-7840.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.