About the Series
GenomeWeb and the Association of Biomolecular Resource Facilities have partnered for the fifth year to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research.
March 30, 2020 | 1:00 PM ET
Computational Approaches for Optimized Nanopore Sequencing Workflows
This webinar features two speakers who will discuss novel computational approaches to optimize sequencing workflows on Oxford Nanopore sequencing platforms.
Our first speaker, Jonathan Foox of the Institute for Computational Biomedicine at Weill Cornell Medicine, will review the rapidly evolving landscape of software to interpret raw Nanopore current data and report modified bases. He will review commonly used and newly available algorithms, and describe the advantages, challenges, and limitations of each. He will also compare base modification call sets generated from Nanopore data against call sets from short-read bisulfite data, as part of the Epigenomics Quality Control study, which aims to describe the reproducibility of genome-wide methylation calling and provide a benchmark of base modification detection across sequencing platforms and library types.
Our second speaker, Miten Jain of the University of California, Santa Cruz, will demonstrate an optimized PromethION nanopore sequencing method that sequenced eleven human genomes on one machine in nine days, using just three flow cells per sample. He will describe computational tools that his team used for this project: Shasta, a de novo long read assembler; and MarginPolish & HELEN, a suite of nanopore assembly polishing algorithms. Dr. Jain will also discuss an evaluation of assembly performance for diploid, haploid, and trio-binned human samples in terms of accuracy, cost, and time and demonstrate improvements relative to current state-of-the-art methods in all areas. He will also discuss how the addition of proximity ligation (Hi-C) sequencing yielded near chromosome-level scaffolds for all eleven genomes.
April 9, 2020 | 1:00 PM ET
Affordable Quantitative Single-Cell Proteomics with SCoPE2
This webinar will discuss SCoPE2 (Single Cell Proteomics by Mass Spectrometry, Version 2), an approach for quantitatively analyzing proteins in single cells using only commercially available equipment and reagents.
Harrison Specht of Northeastern University will share details of the methodology, which lowers cost and hands-on time by introducing automated and miniaturized sample preparation while substantially increasing quantitative accuracy.
Using SCoPE2, Specht and colleagues quantified more than 2,700 proteins in 1,018 single monocytes and macrophages in 10 days of instrument time, and the quantified proteins allowed them to discern single cells by cell type. Parallel measurements of transcripts by 10x Genomics scRNA-seq suggest that SCoPE2 samples 20-fold more copies per gene, thus supporting quantification with improved count statistics. Joint analysis of the data indicated that most genes had similar responses at the protein and RNA levels, though the responses of hundreds of genes differed.
In his presentation, Specht will share details on how researchers can adopt SCoPE2 in their labs. He will discuss equipment that can be used to successfully execute SCoPE2 sample preparation, as well as reagent selection and study design, including the types of cells that are likely to perform well with SCoPE2. Additionally, he will discuss approaches to optimizing liquid chromatography and mass spectrometry instrumentation for SCoPE2 samples.
April 16, 2020 | 1:00 PM ET
Metaproteomics Approaches for Characterizing Human Gut Microbiome Development
This webinar will discuss a mass spectrometry-based metaproteomic approach to examine microbiome temporal functional shifts during microbial colonization of the preterm human infant gut.
Robert L. Hettich of Oak Ridge National Laboratory will discuss his recent work developing advanced “shotgun” mass spectrometry techniques for the comprehensive characterization of microbial metaproteomes. His lab's recent work has focused on improved methods for cellular lysis and proteome extraction, coupled with automated multi-dimensional LC-MS/MS on QExactive mass spectrometric systems. This has been coupled with an improved data analysis/data mining pipeline for enhancing peptide/protein identification and quantification.
Dr. Hettich will discuss a study in which fecal metaproteomes of 94 preterm infant samples, each collected at discrete time points over several months, were measured by LC-MS/MS and yielded identification of tens of thousands of proteins, many of which corresponded to enzymes that mapped onto a large and deeply interconnected network of metabolic reactions.
Tracking metabolic function rather than discrete proteins has the potential of revealing how microbial metabolic function progresses across development of the preterm human infant gut microbiome, and how the overall metabolic potential of the system expands or contracts temporally.
The time-course metaproteomics measurements revealed core metabolic pathways in both human and microbial proteins, indicating the establishment of the mutualistic relationship between the microbiome and human host early in infancy. In total, these results reveal functional stability and inter-individual signatures of the preterm infant gut microbiome.