Today we tried to get RNA from redbud samples. We may need to try again before class on Monday! Tonight, I watched a lightning talk from London Calling 2019 that I had not noticed before. Jungwoo Lee from Yonsei University in the Republic of Korea spoke about “Transcriptome profiling of colon cancer by nanopore sequencing.” The goal of this study was to identify new colon cancer biomarkers. The team obtained samples from healthy and colon cancer. They obtained 23 paired tumor and healthy samples with an average length of cDNA of 800 bp. They used the cDNA-PCR kit and sequenced libraries on the GridION. They filtered out reads that were shorter than 200 bp and were of low quality. Isoforms were identified and differentially expressed non-coding transcripts were analyzed. They attempted to detect fusion gene candidates. Most candidates were multi-copy genes that were being validated. Their data included both Nanopore and Illumina reads. Their analyses and graphs were easy to interpret. I wonder if we can use a similar SQANTI workflow.
