Core lab webinar series: New dimensions of biology revealed by full-length sequencing of single-cell and spatial assays

Event overview

During our first instalment of the series, an amazing set of speakers shared how they are using single-cell nanopore sequencing in the laboratory. To start, Daniel Garalde provided an overview of Oxford Nanopore’s solution for full-length sequencing of single cell and spatial assays. Ruli Gao presented a method for processing high-throughput single-cell nanopore RNA sequencing data and Ruta Sahasrabudhe shared her and her team's experience of sequencing single-cell cDNA libraries on the PromethION.

scNanoGPS achieves independent deconvolution of barcodes and calculates same-cell multi-omic profiles from nanopore single-cell RNA sequencing data

Abstract

Long-read single-cell sequencing is emerging as a powerful approach to perform multi-omic analysis of individual cells. Dr. Ruli Gao will talk about her recent study in developing scNanoGPS, a computational method for processing high-throughput single-cell nanopore RNA sequencing (scNanoRNAseq) data to calculate both genotypic and phenotypic profiles of individual cells. The scNanoGPS method achieves full independence in assigning long-reads into single cells and molecules without guidance of matched NGS data nor barcode whitelist, which greatly simplifies experimental protocol and facilitates data analysis of scNanoRNAseq.

Meet the speaker

Ruli Gao, PhD, is an Assistant Professor of Biochemistry and Molecular Genetics and a member of Robert H. Lurie Comprehensive Cancer Center of Northwestern University. Dr. Gao obtained her Master’s degree in statistics and PhD in genomics at the University of Florida, and received postdoc training at the MD Anderson Cancer Center. Her research is centered around developing single-cell sequencing and computational methods to study tumor evolution models, as well as cellular and molecular mechanisms of diverse human diseases.

Leveraging the PromethION sequencer for single-cell cDNA sequencing in a sequencing core facility

Abstract

The DNA Technologies and Expression Analysis Core offers high-throughput and custom sequencing services on multiple next generation sequencing platforms. We started performing nanopore sequencing on a variety of different sample types using the high throughput PromethION P24 device in 2018 as a part of the PromethION early access program (PEAP). Single-cell RNA sequencing has revolutionized the study of transcriptomics. Long-read sequencing enables the study of full-length transcripts and splice variants providing unique insights into isoform diversity in heath and disease. Over the past two years, we have sequenced several single-cell cDNA libraries on R9 and R10 Flow Cells. The majority of these single-cell cDNA samples were generated using 10X Genomics Chromium platform. We also sequenced cDNA generated using Parse Biosciences SPLit-Seq technology. In this talk we will outline our experience of sequencing these single-cell cDNA libraries on the PromethION

Meet the speaker

Ruta Sahasrabudhe, PhD, is an Assistant Project Scientist in the DNA Technologies and Expression Analysis Core laboratory at the University of California, Davis. Ruta obtained her MBBS degree from the University of Mumbai, India and PhD from the Department of Biological Sciences, University of Pittsburgh, USA. She performed post-doctoral studies in the Carvajal-Carmona lab at UC Davis where she studied cancer genetics. She then joined the DNA Tech Core lab as a research scientist in 2017. Her current work mainly focuses on developing and implementing protocols for long-read DNA and RNA sequencing.