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Universal Sequencing Technology Corporation is a US-based innovative DNA sequencing firm. UST TELL-Seq enables short-read 2nd generation sequencing platforms to produce super long-read results (average 20kb, up to 200kb or longer). It is accurate and cost-effective. The process is simple and fast.

A sequencing-ready library can be prepared in PCR tubes in only 3 hours. With our TELL-Seq library kit and an Illumina sequencer, you can now do de novo sequencing (microbial, animals/plants/insects, etc.), metagenomics, whole-genome phasing, and structural variation detection as well as phased whole-exome and targeted sequencing. The results are proven to be accurate. As significantly cost-effective as UST TELL-Seq is, the technology requires very little DNA input (0.1-0.5ng for bacteria and target gene panels, 3-5ng for human genome).

With a co-marketing and co-development relationship with Illumina signed last year, the TELL-Seq technology is a valuable tool for your genomics research, and it is commercially available now.

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How TELL-SEQ™ Works
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Products

KIT, TELL-Seq Library Reagent Boxes V1 RUO (Standard)
KIT, TELL-Seq Library Reagent Boxes V1 RUO (HT24)
UST TELL-Seq™ Library Multiplex Primer Kits (Sets of 8)
UST TELL-Seq™ (Custom) Illumina® Sequencing Primer Kit
UST TELL-Seq™ Target Blocker 8-Rxn Kit

About Us

Universal Sequencing Technology (UST) was established by a group of NGS technology veterans from Roche/454, dedicated to the development of the most advanced cost-effective DNA sequencing technologies.

Short-read DNA sequencing platforms have dominated the NGS field ever since 2005 when Roche/454 Life Sciences launched the world’s first high throughput NGS sequencing platform. A well-known problem of short-read sequencing is that it cannot do de novo sequencing, and it does not provide the answers that are needed to have a full understanding of genome complexity and to connect health and traits to genome variations.

UST TELL-Seq enables short-read 2nd generation sequencing platforms to produce super long-read results (averaging at 40kb, but up to 200kb or longer). With UST TELL-Seq’s™ proven solution for library prep, a sequencing-ready library can be prepared in PCR tubes in only 3 hours and is highly accurate. As significantly cost-effective as UST TELL-Seq is, the technology requires very little DNA input (0.1-0.5ng for bacteria and target gene panels, 3-5ng for human genome).

This technology allows researchers to do de novo sequencing (microbial, plants, animals, insects, etc.), and to identify structural variations among organisms and individuals more efficiently. Researchers can phase genomes to distinguish parental origins of structural variants. Phasing is particularly important in population genetic studies, newborn and adult health screening, and consumer genetics. In addition to phasing and structural variation analysis, the TELL-Seq kit can be used for metagenomics and analyzing complex mixtures of microbiomes in a wide variety of applications, such as medical microbiomes, environmental microbiomes, marine microbiomes, epidemical surveillance, hospital pathogen monitoring, and food safety.

In the process, Universal Sequencing Technology has filed more than 20 patent applications covering linked read and single-cell library preparation chemistry and groundbreaking 3rd generation DNA sequencing technology.

Universal Sequencing will lead the next wave of DNA sequencing innovations.

How TELL-Seq™ Works

Important publications

Read This: Method of the year: long-read sequencing
Read This: Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen

TELL-Seq™ Technology

UST’s Transposase Enzyme-Linked Long-read Sequencing (UST TELL-Seq™) is a simple and scalable NGS library technology that generates barcode linked-reads for genome-scale sequencing applications. The whole procedure can be carried out in a PCR tube without the need for expensive instrumentation. The TELL-Seq™ Library Prep Kit will generate an Illumina sequencing library in just 3 hours. The protocol can be easily adjusted based on the genome size to be analyzed. TELL-Seq will be the new standard library method for WGS.

TELL-Seq™ Library Preparation and Sequencing Workflow

TELL-Seq Library Preparation and Sequencing Workflow

How It Works

Results

RESULTS I: IGV SNAPSHOT OF TELL-SEQ LINKED READS

RESULTS II: TELL-SEQ RESULTS FOR THREE BACTERIA WITH DIFFERENT GC CONTENT

RESULTS III: DE NOVO ASSEMBLY RESULTS COMPARED WITH REFERENCE

RESULTS IV: WHOLE GENOME HAPLOTYPE PHASING RESULTS

TELL-SEQ™ Library Preparation Kit

Features:

  • Long read NGS library preparation method

  • Easy to use: hands-on time ( < 1 hour)

  • Single tube process: sequencing ready library in 3 hours

  • Low DNA input: 0.5 ng to 5 ng depending on genome size

  • Highly scalable for small and large genomes, 20 Kb to 5 Gb

  • Easily Automated

UST TELL-Seq Library Prep Reagents:

  • TELL-Seq™ WGS Library Reagent Box 1

  • TELL-Seq™ WGS Library Reagent Box 2

  • TELL-Seq™ Multiplexing Primer Kits (sets of 8 or set of 96)

  • TELL-Seq™ Illumina Sequencing Primer Kits

UST TELL-Seq™ Recommended Bundles

UST TELL-Seq™ Recommended Bundles

Research use only. Bundles include enzyme mixes, TELL-Beads™, modified Illumina primers, and multiplexing primers.

Microbial & Small Genomes - up to 50 Mb

Standard Bundle (STD8)

The standard bundle has enough reagents to prepare four (4) sample libraries for genomes 1 Gb or larger for both diploid and haploid genomes.

The standard bundle includes the following:

  • UST TELL-Seq Microbial Library Reagent Box 1, V1 RUO

  • UST TELL-Seq Microbial Library Reagent Box 2, V1 RUO

  • UST TELL-Seq™ Library Multiplex Primer Set (1-8),

  • UST TELL-Seq™ (Custom) Illumina® Sequencing Primer Set

Standard Bundle (STD8)

Standard Bundle (STD24)

The standard bundle has enough reagents to prepare four (4) sample libraries for genomes 1 Gb or larger for both diploid and haploid genomes.

The standard bundle includes the following:

  • UST TELL-Seq Microbial Library Reagent Box 1, V1 RUO

  • UST TELL-Seq Microbial Library Reagent Box 2, V1 RUO

  • UST TELL-Seq™ Library Multiplex Primer Set (1-8)

  • UST TELL-Seq™ Library Multiplex Primer Set (9-16)

  • UST TELL-Seq™ Library Multiplex Primer Set (17-24)

  • UST TELL-Seq™ (Custom) Illumina® Sequencing Primer Set*

Standard Bundle (STD24)

High-Throughput Bundle (HT144)

The high-throughput bundle has enough reagents to prepare 144 sample libraries for genomes 1 Gb or larger for both diploid and haploid genomes.

The high-throughput bundle includes the following:

  • UST TELL-Seq Microbial Library Reagent Box 1 HT, V1 RUO

  • UST TELL-Seq Microbial Library Reagent Box 2 HT, V1 RUO

  • UST TELL-Seq™ Library Multiplex Primer C-series (1-96) Plate

  • UST TELL-Seq™ Modified Illumina® Sequencing Primer Set (HT)*

High-Throughput Bundle (HT144)
TELL-Seq™ Microbial WGS Library Prep User Guide

Large Genomes - 1Gb or more (5Gb+)

Standard Bundle (STD4)

The standard bundle has enough reagents to prepare four (4) sample libraries for genomes 1 Gb or larger for both diploid and haploid genomes.

The standard bundle includes the following:

  • UST TELL-Seq™ Library Prep Reagent Box 1 V1 RUO

  • UST TELL-Seq™ Library Prep Reagent Box 2 V1 RUO

  • UST TELL-Seq™ Library Multiplex Primer Set (1-8),

  • UST TELL-Seq™ (Custom) Illumina® Sequencing Primer Set

Standard Bundle (STD4)

High-Throughput Bundle (HT24)

The high-throughput bundle has enough reagents to prepare 24 sample libraries for genomes 1 Gb or larger for both diploid and haploid genomes.

The high-throughput bundle includes the following:

  • UST TELL-Seq™ Library Prep Reagent Box 1, HT24, V1 RUO

  • UST TELL-Seq™ Library Prep Reagent Box 2, HT24, V1 RUO

  • UST TELL-Seq™ Library Multiplex Primer Set (1-8)

  • UST TELL-Seq™ Library Multiplex Primer Set (9-16)

  • UST TELL-Seq™ Library Multiplex Primer Set (17-24)

  • UST TELL-Seq™ Modified Illumina® Sequencing Primer Set (HT)*

High-Throughput Bundle (HT24)

High-Throughput Bundle (HT96)

The high-throughput bundle has enough reagents to prepare 96 sample libraries for genomes 1 Gb or larger for both diploid and haploid genomes.

The high-throughput bundle includes the following:

  • 4x UST TELL-Seq™ Library Prep Reagent Box 1, HT24, V1 RUO

  • 4x UST TELL-Seq™ Library Prep Reagent Box 2, HT24, V1 RUO

  • UST TELL-Seq™ Library Multiplex Primer C-series (1-96) Plate

  • 2x UST TELL-Seq™ Modified Illumina® Sequencing Primer Set (HT)*

High-Throughput Bundle (HT96)

*YOU MAY NEED MORE TELL-SEQ™ MODIFIED ILLUMINA® SEQUENCING PRIMER SETS BASED ON YOUR SYSTEM/CONFIGURATION. PLEASE CONTACT INFO@STRATECH.CO.UK TO VERIFY THE QUANTITIES NEEDED BEFORE PURCHASING.

Products

KIT, TELL-Seq Library Reagent Boxes V1 RUO (Standard)

KIT, TELL-Seq Library Reagent Boxes V1 RUO (Standard)

Research Use Only. Multiplexing primers and modified Illumina primers are sold separately.

Product Catalogue No. Product Description
100035 Box 1 – Enzyme Mixes (Standard)
100036 Box 2 – TELL-Beads™ (Standard)

KIT, TELL-Seq Library Reagent Boxes V1 RUO (HT24)

KIT, TELL-Seq Library Reagent Boxes V1 RUO (HT24)

Research Use Only. Multiplexing primers and modified Illumina primers are sold separately.

Product Catalogue No. Product Description
100037 Box 1 – Enzyme Mixes (HT24)
100038 Box 2 – TELL-Beads™ (HT24)

UST TELL-Seq™ Library Multiplex Primer Kits (Sets of 8)

UST TELL-Seq™ Library Multiplex Primer Kits (Sets of 8)

Research Use Only. Multiplex primers to be used with the UST TELL-Seq™ Library Prep Kit (up to 48 reactions per box).

Product Catalogue No. Product Description
100003 Set 1-8
100009 Set 9-16
100010 Set 17-24

UST TELL-Seq™ (Custom) Illumina® Sequencing Primer Kit

UST TELL-Seq™ (Custom) Illumina® Sequencing Primer Kit

Research Use Only. Customized Illumina® sequencing primers to be used with the UST TELL-Seq™ WGS Library Prep Kit. (Up to 16 reactions depending on sequencer)

Product Catalogue No. Product Description
100004 Standard Kit
100013 High-Throughput (HT) Kit

UST TELL-Seq™ Target Blocker 8-Rxn Kit

UST TELL-Seq™ Target Blocker 8-Rxn Kit

Research Use Only. To be used with the UST TELL-Seq™ WGS Library Prep Kit for targeted applications.

Product Catalogue No. Product Description
100019 Standard Kit

TELL-Seq™ Library Multiplex Primer C-series (1-96) Plate

TELL-Seq™ Library Multiplex Primer C-series (1-96) Plate

Research Use Only. Multiplex primers are used with the UST TELL-Seq™ Library Prep Kit (up to 384 reactions per box).

Product Catalogue No. Product Description
100043 (1-96) Plate

Applications

DE NOVO ASSEMBLY

Using the TELL-Seq™ WGS library prep kit you can sequence novel genomes. This works for small bacterial genomes, medium sized insect, plant, and fungi genomes and large animal and plant genomes. The TELL-Seq™ kit will turn an ordinary short-read 2nd generation DNA sequencer into a long-read 3rd generation DNA sequencer. If you really want to understand a new genome, including gene synteny, you must look at long-reads.

METAGENOMICS SEQUENCING

Samples containing disparate microbes are essential to gaining insight into our ecosystem as well as human disease. The TELL-Seq™ WGS Library Prep kit will allow you to sequence samples at a metagenomic scale; providing long-read like results with the ease of short-read sequencing. To see what is truly in a mixed microbial sample use the power of long-read DNA sequencing with the simplicity of short-read sequencing.

STRUCTURAL VARIATION

Short-read DNA sequencers have trouble identifying large structural variants. These could be in the form of copy number variants, translocations, duplications, deletions, insertions, and inversions. The TELL-Seq™ WGS Library Prep kit links short-reads turning them into long-reads. The linked, long-read data that you get using the TELL-Seq™ kit will allow you to take a step back and see what you were missing.

WHOLE GENOME PHASING

Knowing which homologous chromosome has which sequence is essential to understanding a genome. Whole Genome Phasing is difficult with 2nd generation, short-read, DNA sequencing technology. Phasing provides haplotype information which is important for understanding complex traits and variant linkages. The TELL-Seq™ WGS DNA Library Prep kit helps with this by linking short-reads to larger fragments and therefore long-reads.

Resources

High-Molecular-Weight DNA Preparation & Recommended HMW DNA Extraction Kits

High-Molecular-Weight (HMW) DNA Preparation:

A Crucial Step for Linked-Read Sequencing

IMPORTANCE OF HMW DNA FOR ULTRA-LONG LINKED-READ GENOMIC SEQUENCING AND GUIDANCE ON PRESERVING HMW DNA DURING SAMPLE AND LIBRARY PREPARATION (RECOMMENDED HMW DNA EXTRACTION KITS BELOW)

Introduction

Linked-read genomic sequencing is a next-generation sequencing (NGS) technology that enables the analysis of large genomic regions with a high degree of accuracy. One key aspect of this technology is the use of high-molecular-weight DNA, which refers to large and complex DNA molecules. These large DNA molecules are essential for linked-read genomic sequencing, as they provide a more complete and accurate representation of the genome. However, preserving and handling high-molecular-weight DNA can be challenging, as it is prone to degradation and damage during sample processing. Therefore, it is critical to take care when processing samples to preserve the high-molecular-weight DNA.

Benefits

Linked-read genomic sequencing relies on using DNA barcodes, which are short DNA sequences attached to the ends of the DNA fragments being sequenced. These barcodes serve as unique identifiers for each fragment, allowing the sequencer to link the fragments together and reconstruct the original genomic region. However, this reconstruction is only possible if the DNA fragments are large enough to contain a sufficient number of barcodes. High-molecular-weight DNA molecules are ideal for this purpose, as they are typically larger and more complex than smaller DNA molecules.

In addition to enabling the reconstruction of genomic regions, high-molecular-weight DNA also provides a more accurate genome representation. This is because large DNA molecules are more likely to contain diverse genomic features, such as repetitive elements, structural variants, and epigenetic modifications. These features are important for understanding the function and regulation of the genome, and their absence or oversimplification can compromise the accuracy of genomic analyses.

Challenges

Despite the benefits of high-molecular-weight DNA for linked-read genomic sequencing, preserving and handling these large DNA molecules can be challenging. One of the main challenges is that high-molecular-weight DNA is prone to degradation and damage during sample processing. Various factors, such as mechanical shearing, chemical degradation, and enzymatic cleavage, can cause this. For example, using mechanical shears or sonication to fragment DNA can result in the loss of large DNA molecules, while enzymes such as DNases can cleave the DNA into smaller fragments.

To preserve the high-molecular-weight DNA, it is essential to minimize the exposure of the DNA to these damaging factors during sample processing. This can be achieved by using gentle methods for DNA fragmentation, such as enzymatic digestion or microfluidic bead-based fragmentation. It is also essential to use specialized reagents and equipment designed to minimize the risk of DNA degradation and damage.

Another challenge in preserving and handling high-molecular-weight DNA is maintaining the DNA molecules’ integrity throughout the entire sample processing workflow. This includes steps such as DNA purification, library preparation, and sequencing. Any loss or damage to the DNA during these steps can compromise the quality and accuracy of the genomic data. To ensure the integrity of the DNA molecules, it is essential to use optimized protocols and carefully follow best practices for sample handling and storage.

Conclusion

High-molecular-weight DNA is a critical component of linked-read genomic sequencing, as it enables the reconstruction of large genomic regions with high accuracy. However, preserving and handling these large DNA molecules can be challenging due to their vulnerability to degradation and damage. Therefore, it is essential to take care when processing samples to preserve the high.

FAQs

TELL-Seq™ WGS Library Prep Kit FAQs:

TELL-Seq™ WGS Library Prep Kit FAQs:

I would like to try the TELL-Seq kit on my samples what do I need to order?

Our standard TELL-Seq WGS library prep kit is made up of two boxes (#100001 & #100002). We also offer a high throughput kit (HT24) that allows the user to make 6-times the number of libraries. Whether you order our standard kit or our HT24 kit you will also need Multiplex primers (#100003, #100009, and/or #100010) and Sequencing primers (#100004 or #100011).

How many samples can be run with one TELL-Seq kit?

One standard TELL-Seq kit along with the associated primers can be used to prepare 12 samples/libraries from microbial genome samples or 4 samples/libraries from Human genomes samples. The number of libraries that can be prepared with one kit depends on the size of the genome of your organism of choice. If you have a large project with 10s to 1000s of samples, you should use our TELL-Seq HT24 kit.

Do I need special sequencing primers or sequencing reagents?

If you are routinely preparing short-read NGS samples in your laboratory you likely have all of the equipment and instrumentation needed for, TELL-Seq. When ordering TELL-Seq kits you will also order sequencing primers. These primers can be used to prepare libraries compatible with all common Illumina sequencing systems including MiSeq, MiniSeq, NextSeq, HiSeq, and NovaSeq. The primers do not interfere with the default sequencing primers if a mixture of libraries is being sequenced on a flow cell.

How much sample DNA do I need for each library prep?

For Human genomes, you only need 5 ng of DNA and for microbial genomes as little as 0.1 ng. The TELL-Seq kit is great for people who want a long-read-like result but have very little sample.

What are Linked-Reads?

Linked-reads involve reading DNA sequences in a short-read sequencer (e.g., Illumina sequencer) and then using a unique barcode to label an intact, high molecular weight DNA molecule before processing further into a standard short-read sized library fragment. If two short DNA segments (300 bp) are near each other on a longer DNA segment (50,000 bp) they may be identified as linked. Linked-read DNA sequencing allows a researcher to work back to the original longer DNA segment due to the barcoding that occurs pre-capture.

How long are the barcodes, and what is their structure?

TELL-Seq barcodes are 18-base in length of semi-degenerate bp composition. The pool is biased away from polynucleotide sequences that are challenging with two color chemistries. The typical sequencing profile of a barcode pool looks like following:

How is Linked-Read DNA sequencing performed?

There are a few ways that Linked-read DNA sequencing can be performed. One way to do this is through compartmentalization of long DNA segments. If you can isolate a long DNA segment into a micro compartment, like a droplet, you can then break the long segment into small segments and give each one a barcode. If the components of the original long DNA segment have the same barcode, then they are “linked”. The TELL-Seq method does not use droplets, but instead uses a much more elegant approach with beads.

What’s the key difference for the library making between TELL-Seq and, stLFR and 10X?

The major difference among these methods is the barcoding method. The 10x Genomics barcoding happens in a water-in-oil droplet, which requires an instrument for droplet generation. Neither TELL-Seq nor stLFR™ uses droplets for barcoding. Instead, the barcoding reactions happen in an open environment and are partitioned using beads alone. TELL-Seq and stLFR™ use different transposases, barcode system, and barcoding method. TELL-Seq enables all the reactions in a PCR tube, which is easy for scaling up to prep multiple samples and for automation.

How many DNA fragments are there per bead?

We have worked out the optimal ratios of DNA molecules, enzymes, barcode-containing beads. For small genomes (<200 Mb), the average number of DNA fragments per bead is 3 to 4. For large genomes, the average is more like 6 to 8 DNA fragments per bead. Obviously, with more than one fragment per bead you will run into “barcode collision” events, but that is okay. Even with the small amount of DNA input, there will be plenty of redundancy. This redundancy provides enough information for the pipeline to workout which reads are part of a larger DNA segment.

What is the percentage of barcodes typically assigned to linked reads?

TELL-Seq sequencing can generate many more barcodes than expected due to sequencing error primarily. These extra barcodes can account anywhere from 40% to 70% of total barcode population in a sequencing run. However, these barcodes are associated with 1 or 2 reads usually and won’t be useful as linked reads. The total reads associated with this kind of barcodes are <5% of all sequencing reads.

Will TELL-Seq technology work with PCR fragments of approximately 1000 bp or larger?

TELL-Seq technology can work with long PCR fragments from a haploid or diploid sample, preferably >4kb. The longer the DNA fragment, the more impactful the resultant TELL-Seq data set.

Are the subreads discontinuous like in the initial cartoon? What is a typical read length following assembly?

Yes, linked reads are not contiguously long sequencing reads. They are scattered short reads across a DNA molecule. Linked read DNA molecule length depends on the input DNA quality significantly as well as careful mixing up through the amplification reaction. For a HMW DNA sample after TELL-Seq, greater than 90% sequenced linked read molecule length is over 20kb and up to 200 Kb.

What is the best way to prepare the DNA for the TELL-Seq kit?

The most important thing you can do to assure you get great results with the TELL-Seq kit is to provide high molecular weight (HMW) double-stranded DNA as your input material. The longer the starting material the longer the reads, and the richer the information. DNA fragments >20 kb in length are the suggested minimum fragment size to see a benefit of using TELL-Seq kits, but if possible try to isolate fragments >100 kb in length. The best method for HMW isolation depends on your sample type. If your laboratory routinely isolates DNA for other HWM applications such as optical mapping, BAC library creation, or long-read sequencing platforms, your existing methodologies are likely fine. If you are new to HMW DNA isolation, we recommend isolating HMW DNA with a commercial kit and our tech support team would be happy to discuss kit options once we understand your project.

What is the binding capacity per bead?

The beads have a high binding capacity, but we have worked out the ratios so that the beads are not overwhelmed. However, if you do provide very long DNA segments as the starting material, the beads can handle it. After analysis, the average linked read molecule length is >50 kb and generally is in the range of 20 kb to 200 kb.

How do you reconstruct the long DNA fragments?

With our pipeline software (TELL-Read, TELL-Sort, and TELL-Link). The TELL-Seq method doesn’t reconstruct each long DNA fragment at the individual left. It relies on the redundancy of long DNA segments, an optimized ratio of DNA molecules to beads, and the known probability of transposon-based insertion. Our software takes this jumble of small reads and barcodes and informatically stitches into the long-range sequencing information from TELL-Seq reads.

Can I mix multiple libraries together for sequencing?

Yes. How to mix different libraries for sequencing depends on how many libraries, the size of the genomes, and sequencer output. For instance, if you wanted to have libraries from three fish species together in one run and their genome sizes are similar, you can pool them so that they are equimolar for sequencing on a high throughput sequencing system.  Mixing samples of greatly different genome sizes on the same lane is more complex and should only be attempted once you have familiarity with our assay.

Can I use TELL-Seq data with other long-read pipelines?

Our customers have found that using TELL-Seq data to scaffold assemblies generated by other long-read sequencing technology significantly improves the long-read assembly results. In addition, TELL-Seq data can also be used as the first step for a de novo sample to estimate the genome size before further sequencing with long-read technology.

Can I use TELL-Seq libraries as a starting point for targeted enrichment?

We now sell blocking oligos that are compatible with Agilent SureSelect™. Prepare the TELL-Seq library as normal and use our blocking oligos during the hybridization step in place of the Agilent blockers.

Webinars

On-demand Webinars:

Human commensal Candida albicans strains demonstrate substantial within-host diversity and retained pathogenic potential

TERESA O’MEARA PHD LAB, UNIVERSITY OF MICHIGAN, DEPARTMENT OF MICROBIOLOGY & IMMUNOLOGY

IDENTIFYING GENOME-WIDE STRUCTURAL VARIATION WITH UST TELL-SEQ™

Candida albicans is a frequent colonizer of human mucosal surfaces and an opportunistic pathogen. C. albicans is remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availability, pH, immune responses, and resident microbes, among other cues. It is still being determined how the genetic background of a commensal colonizing population can influence the shift to pathogenicity. Therefore, we examined commensal isolates from healthy donors to identify site-specific phenotypic adaptation and genetic variation associated with these phenotypes. We demonstrate that healthy people are reservoirs for genotypically and phenotypically diverse C. albicans strains and that this genetic diversity includes SNVs and structural rearrangements. Using limited diversity exploitation, we identified a single nucleotide change in the uncharacterized ZMS1 transcription factor that was sufficient to drive hyper invasion into agar. However, our commensal strains retained the capacity to cause disease in systemic infection models, including outcompeting the SC5314 reference strain during systemic competition assays. This study provides a global view of commensal strain variation and within-host strain diversity of C. albicans. It suggests that selection for commensalism in humans does not result in a fitness cost for invasive disease.

Wet Lab Best Practices

Preserving High-Molecular Weight DNA and Molecular Information 200 Kb or more

Gaining insight into genetic information at the molecular level up to 200 Kb or more is made possible with UST TELL-Seq’s™ proven library preparation technology which has been providing this capability to researchers looking for ultra-long-range results for years.

However, when it comes to getting this information from your sequencer, care must be taken during the preparation and handling of DNA when making libraries with UST TELL-Seq™. With years of experience working to preserve this molecular information, the team at Universal Sequencing has identified several areas of the process where extra care should be taken, and solutions to challenges users sometimes face.

Library Preparation and Genome Assembly Using Transposase Enzyme-Linked Long-Read Sequencing (UST TELL-Seq)

In this webinar, Alvaro Hernandez, Ph.D., director of DNA Services at the University of Illinois at Urbana Champaign, will discuss how his team sequenced and assembled the genomes of nine insects using Transposase Enzyme-Linked Long-Read Sequencing (TELL-Seq) at different stages of genome assembly. The unique contributions of TELL-Seq libraries to the completeness of the assembly, as well as the DNA extraction, library preparation, and sequencing methods the team employed, will be discussed in detail.

The insect genomes were sequenced as a pilot project from the University of Illinois Prairie Research Institute, Carl R. Woese Institute for Genome Biology, and the Roy J. Carver Biotechnology Center to demonstrate the potential for Illinois to join a global network of communities engaged in genome assembly and the conservation of biodiversity.

Illumina recently entered into a partnership with Universal Sequencing Technologies, the inventor and distributor of TELL-Seq products, and is sponsoring this webinar to raise awareness of the applications of this novel sequencing technology.

Haplotype Phasing of PCR Amplicons using UST TELL-Seq

Haplotype phasing of genomes and de novo assembly of novel genomes are major hurdles for short read based next generation sequencing platforms. Long sequence reads are essential to overcome the significant sequence homology on some regions of the genome. Several NGS library technology breakthroughs recently have demonstrated barcode linked-read sequencing method can effectively generate long read like information and successfully applied for human genome phasing, structural variation detection or de novo assembly of other genomes. However, they either require expensive capital expenditure on a special instrument or are not scalable for commercial adoption yet due to sophisticated barcode generation. We have developed a simple and scalable NGS library technology, Transposase Enzyme Linked Long-read Sequencing (TELL-SeqTM), to use short NGS reads for genome scale haplotype phasing and/or de novo genome assembly. Several million uniquely barcoded beads are used to generate linked reads, which could be linked as long as a hundred kilobases, by strand transfer reactions using transposase in a PCR tube with a standard NGS laboratory setting. TELL-Seq library procedure takes approximately 3 hours and multiple samples can be easily processed parallelly in a 96-well format when needed. The library protocol can be adjusted and used for various sizes of genomes from bacteria to human. Using TELL-Seq we are able to generate comparable and excellent haplotype phasing results on a NA12878 human sample, and successfully de novo assembly on an E. coli and an Arabidopsis thaliana. More applications and analysis solutions are being developed for TELL-Seq library technology.

Visualization of UST Tell-Sort Data Using the Integrative Genome Viewer

Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today’s sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.

Recorded Presentations:

Introduction to Next-Gen, Super-Long-Linked-Read using UST TELL-Seq

Deep-dive: UST TELL-Seq’s Super-Long-Linked-Read Technology