Introduction: Comprehensive characterization of RNA isoforms is essential for understanding transcriptomic complexity but remains limited by short read sequencing technologies. To address this, we have developed an integrated bulk and single-cell long read RNA sequencing framework, combining optimized wet lab workflows with scalable, end to end dry lab pipelines to enable isoform resolved analysis from tissues to individual cells.

Methods: At the wet lab level, protocols are optimized to generate high quality, full length cDNA libraries, to ensure faithful preservation of transcript structure across both bulk and low input single cell settings. These experimental workflows form the foundation for robust downstream analysis, emphasizing transcript completeness, coverage, and reproducibility.

Results: Complementing these efforts, we have built two modular Nextflow based pipelines—one for bulk long read RNA seq and one for single-cell long read RNA seq—following a shared design philosophy of robustness, reproducibility, and scalability. The bulk pipeline supports comprehensive transcriptome profiling and isoform discovery. The single-cell pipeline extends this capability to cellular resolution, integrating barcode handling to deliver interpretable outputs. We are also exploring the use of AI tools to evaluate model-specific detection of novel transcripts.

Conclusion: Together, these pipelines translate raw long-read data into biologically actionable insight and enable consistent application across diverse experimental contexts. Initial applications include support for oligonucleotide therapeutic research, where isoform level resolution informs RNA target landscapes; translational preclinical models, where improved transcript annotation enhances cross species interpretability. This end-to-end long read framework provides a flexible foundation for integrating transcript structure into modern omics driven target and drug discovery.