Set5: HCC single-cell Loop-seq long-read RNA-seq by Element Biosciences AVITI platform

DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts. Overall design: HCC samples and benign liver samples were freshly dissected from a patient who underwent liver transplantation. Long-read single-cell transcriptome sequencing was performed by LoopSeq, Element Biosciences. Each library (tumor or benign) was sequenced by four runs and eventually pooled together. Same sample as we did in GSE223743, but sequenced with Element Biosciences AVITI machine.