We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us
Technopath Clinical Diagnostics - An LGC Company

Download Mobile App




Events

ATTENTION: Due to the COVID-19 PANDEMIC, many events are being rescheduled for a later date, converted into virtual venues, or altogether cancelled. Please check with the event organizer or website prior to planning for any forthcoming event.
01 Mar 2023 - 03 Mar 2023

Ultima Genomics Sequencer for Single-Cell RNA-Seq Evaluated

By LabMedica International staff writers
Posted on 19 Sep 2022
Print article
Image: The UG100 sequencer used for single-cell RNA sequencing (Photo courtesy of Ultima Genomics)
Image: The UG100 sequencer used for single-cell RNA sequencing (Photo courtesy of Ultima Genomics)

Single-cell RNA sequencing (scRNA-seq) enables the study and characterization of cellular states and pathways at ever-growing investigational scales, including the Human Cell Atlas, cell atlases for tumors and other diseases, and large-scale Perturb-Seq screens of millions of cells under genetic or drug perturbations.

Mostly natural sequencing-by-synthesis (mnSBS) is a new sequencing chemistry that relies on a low fraction of labeled nucleotides, combining the efficiency of non-terminating chemistry with the throughput and scalability of optical endpoint scanning within an open fluidics system to enable high-throughput sequencing.

Genomic Scientists at the Broad Institute (Cambridge, MA, USA) and their colleagues devised a library preparation method to run single-cell libraries generated with 10x Genomics' Chromium platform (Pleasanton, CA , USA) on the Ultima Genomics UG100 instrument (Newark, CA, USA), which produces single-end, rather than paired-end, reads. The method uses a PCR-based kit to convert the 10x libraries, which are designed to run on Illumina sequencers (Illumina, San Diego, CA, USA), for use with the Ultima sequencer.

The scientists demonstrated successful application in four scRNA-seq case studies of different technical and biological types, including 5′ and 3′ scRNA-seq, human peripheral blood mononuclear cells (PBMC) from a single individual and in multiplex, as well as Perturb-Seq. Benchmarking shows that results from mnSBS-based scRNA-seq are very similar to those using Illumina sequencing, with minor differences in results related to the position of reads relative to annotated gene boundaries, owing to single-end reads of Ultima being closer to gene ends than reads from Illumina.

Of the 166 genes with differences in expression for 3′ PBMC between the two sequencing platforms, most (130 genes, 78.3%) differed in the fraction of reads that were assigned by Cell Ranger to the gene out of all the reads mapped to that gene region. This suggests that this is related to how single- and paired-end reads map to different locations relative to the transcript. Ultima reads map closer to the 5′ and 3' end than do Illumina reads. Because Cell Ranger excludes reads that do not fully map within annotated gene boundaries, more Ultima reads are excluded from analysis as they are closer to gene ends. This difference in location can also lead to more multimapping or ambiguous reads.

Gilad Almogy, PhD, Ultima CEO and Cofounder, said, “The UG100 is a generic sequencing platform and is capable of accommodating most existing sequencing libraries, including libraries prepared for other platforms via a simple conversion process. Specifically, we've successfully tested sequencing of 10x single cell ATAC-seq and CITE-seq libraries, as well as other single-cell labeling approaches.”

Joshua Levin, PhD, a senior author of the study, said , “Given that it would be a lower cost, other issues would not be a problem that would prevent you from using Ultima, and that for some applications, such as T- and B-cell receptor sequencing, 5' approaches are required. Ultima has claimed it can deliver NGS of equivalent accuracy to Illumina at approximately USD 1 per Gb, compared to approximately USD 6 to USD 7 per Gb, list price, for Illumina's highest throughput NovaSeq instrument. You can change the scale of your screen.”

The authors concluded that the method was compatible with state-of-the-art scRNA-seq libraries independent of the sequencing technology. They expect mnSBS to be of particular utility for cost-effective large-scale scRNA-seq projects. The study was published on September 15, 2022 in the journal Nature Biotechnology.

Related Links:
Broad Institute
10x Genomics
Ultima Genomics
Illumina

Gold Supplier
Group A Streptococcus Antigen Test
OSOM Strep A Test
New
Lateral Flow Assay Pads
POREX Sample Pads
New
Dengue lgG/lgM Rapid Test
Dengue Rapid Test (Colloidal Gold Method)
New
Procalcitonin Test
RAMP PROCALCITONIN Test

Print article
MEDLAB - INFORMA

Channels

Immunology

view channel
Image: Scientists have won USD 9.5 million to study emerging pathogens (Photo courtesy of Pexels)

Study of Emerging Pathogens to Better Understand Influenza-Antibody Interactions Could Improve Diagnostics

Outbreaks of Avian influenza have occurred around the world for over a century. The highly pathogenic H5N1 virus which was first identified in 1996 can lead to severe disease and has a high fatality rate... Read more

Microbiology

view channel
Image: Medical illustration of Carbapenem-resistant Enterobacteriacea (Photo courtesy of CDC, Stephanie Rossow)

Breakthrough Test Enables Targeted Antibiotic Therapy for Various Enterobacter Species

Bacteria of the Enterobacter genus are considered to be the most dangerous bacteria linked to hospital infections across the world. Some of their representatives demonstrate high resistance to commonly-used... Read more

Technology

view channel
Image: Flexible copper sensor made cheaply from ordinary materials (Photo courtesy of University of São Paulo)

Low-Cost Portable Sensor Detects Heavy Metals in Sweat

Heavy metals like lead and cadmium can be found in batteries, cosmetics, food and many other things that have become a part of daily life. However, they become toxic if they accumulate in the human body... Read more
Copyright © 2000-2023 Globetech Media. All rights reserved.