The UMGC is pleased to now offer long-read sequencing on the PacBio Sequel platform. Released in mid-2016, the Sequel is PacBio’s most recent instrument, and uses single-molecule real-time (SMRT) technology to generate reads with modal lengths of 8-10 kb. With recently introduced “V2” chemistry and “V4” software, mean reads lengths are reported to increase to 10-18 kb, with half of data in reads > 20kb and read lengths up to 80 kb possible. One SMRT cell “run” on the Sequel generates between 5-8 Gb of primary data. The Sequel’s long reads are particularly suited to genome assembly, microbial genomics, detection of structural variants, and transcriptional isoform sequencing (Iso-Seq).
The innovative Chromium instrument from 10X Genomics is an emulsion-tagging library creation platform that can be used for both DNA-based and single-cell RNA-based applications. For DNA Chromium creates “linked reads” (barcoded sets of reads) from single, ultra-long molecules. These linked reads can be used for whole-genome phasing, structural variant detection, and de novo genome assembly. The Chromium platform thereby extends the utility of Illumina sequencing into the realm of long-read data generation. In its “single-cell genomics” format, the 10X Chromium uniquely tags transcripts from single cells to enable affordable single-cell gene expression analysis of between 200-10,000 cells per run.
We provide microbiome marker gene (bacterial 16S, fungal 18S and ITS1/ITS2) survey analysis, beginning from crude biological samples (feces, other human fluids, soil samples, etc.) or from extracted DNA. Our technology is based on UMGC-developed dual-indexing PCR methods, that in a recent report in Nature Biotechnology were shown to provide more quantitatively accurate and qualitatively complete measurement of controlled mock communities than other commonly used protocols. Marker-gene sequencing is typically carried out using the Illumina MiSeq platform, but deep sequencing for metagenomic and meta-transcriptomic methods is also available.
Sequence-Based Genotyping (SBG) is an affordable “reduced representation” next-generation sequencing method for genotyping DNA from any source, without the need for arrayed content or targeted primers. The UMGC has obtained a license from KeyGene to provide this proprietary technology for both local UMN and external academic and commercial clients. SBG is ideal for the genetic characterization of species for which there are no well-established reference maps or commercially-available targeted reagents. We provide a complete sample-to-genotype workflow, including bioinformatic analysis and high-throughput DNA extraction when needed.