Genomic Sequencing 

The CMMR is a CLIA Certified Laboratory (CLIA #45D2111954) that follows federal standards for the analysis of human specimens. We operate automated platforms for sample processing, library preparation, and quality control. Our sequencing platforms include the PacBio long read sequencing platform and the Illumina short read platforms: iSeq, MiSeq, NextSeq, HiSeq and NovaSeq. The CMMR also maintains a collaborative support from the Human Genome Sequencing Center at Baylor College of Medicine for the use of a few high-throughput next generation sequencing (NGS) systems. 

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Illumina NovaSeq 6000 Sequencing System

The NovaSeq platform is a powerful instrument capable of sequencing anywhere from 167 billion bases in a single flow cell up to 6 trillion bases in a single run. This new technology supports microbiome applications for any sequencing method, species and scale at a very low cost per sample. See Illumina NovaSeq specifications for further information.

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Illumina HiSeq 3000 Sequencing System

The Illumina HiSeq 3000 sequencer is designed for processing more samples in greater depth to generate richer, more meaningful data to accomodate a wide range of ultra-high throughput sequencing applications. Its flow cell features a capacity of processing over 200 Gb per day or 750 Gb per run, with up to 2.5 billion single reads from microbiome samples. Check the Illumina HiSeq 3000 Specifications for further information. 

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Illumina HiSeq X Sequencing System

The HiSeq X system can sequence the human genome at 30x coverage or greater. It is also very cost-effective WGS for non-human species, thus enabling research in many areas including the microbiome, agriculture and model organism research. Visit Illumina HiSeq X Specifications for further information. 

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Illumina NextSeq Sequencing System

The NextSeq 550 System is efficient and flexible to handle a range of different types of projects. It delivers on-demand whole-genome, transcriptome, and targeted resequencing applications with a rapid, one-day turnaround. Easily switch between two flow cell configurations to tune your output based on your current research needs for microbiome applications or sample batch sizes. Check the Illumina NextSeq Specifications for further information.

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Illumina MiSeq Sequencing System

The MiSeq system performs the widest breadth of sequencing applications, including highly multiplexed PCR amplicon sequencing, small genome resequencing and de novo sequencing, small RNA sequencing, library quality control, and 16S metagenomics. This system is used for small genome sequencing and comprehensive analysis of microbial or viral genomes for public health, epidemiology, and disease studies. Read the Illumina MiSeq Specifications for further information.

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Illumina MiSeqDX Sequencing System

The MiSeqDx System delivers a broad range of sequencing applications and it has been used in our lab for microbiome studies. Illumina offers two FDA-cleared cystic fibrosis assays and an FDA-approved companion diagnostic to aid in the identification of patients with colorectal cancer. See the Illumina MiSeqDX Specifications for further information.

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Illumina iSeq 100 Sequencing System

It is the smallest Illumina sequencing instrument and it delivers faster and more cost-effective benchtop sequencing solution for our collaborators. The iSeq 100 provides up to four million reads in about 17 hours for a 2x1500 basepair run. This supports a wide array of microbiome applications such as viral sequencing, small panels, and small whole genomes. Check the Illumina iSeq 100 Specifications for further information.

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PacBio SMRT Sequencing System

This system provides high-quality sequencing for genomes, transcriptomes and epigenomes through long-read sequencing and high consensus accuracy for your microbiome study. Read the PacBio SMRT Specifications for further information.

Supporting Equipment

Technology and automation continue to integrate in our core with the main objective to increase speed, raise productivity, improve efficiency, deliver better quality, lower costs and reduce errors. Below is a list of some essential equipment to improve and support the genome sequencing workflow within our facility: 

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Labcyte Echo 525 Acoustic Liquid Handler

The Echo 525 Liquid Handler transfers a wide range of fluids including distilled water, buffers, nucleic acids, and reagents containing up to 50% glycerol. The Echo acoustic droplet ejection (ADE) technology is based on sound waves to eject precisely-sized droplets from the source plate onto the destination plate. It is a powerful equipment that supports a wide range of genomic assays.

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Automated Liquid Handling

Automated liquid handling robots dispense and sample liquids in tubes or wells, which are critical for labor saving devices and offer precision sample preparation for high throughput screening/sequencing (HTC), liquid or powder weighing, sample preparation, and bio-assays of many kinds.

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Biomek Liquid Handler

This compact liquid handler can work with two pipetting models: Multichannel (96 or 384) or Span-8. Both combine the benefits of a small footprint with the increased efficiency and flexibility of a medium- to high-throughput instrument capability based on the workflow needs.

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Fragment Analyzer

The Fragment Analyzer is a parallel capillary electrophoresis instrument designed to eliminate laboratory bottlenecks caused by slow and unreliable QC analysis of nucleic acids. These bottlenecks are resolved by the automation of key steps such as gel loading and sample injection. After separations are complete, nucleic acid fragment analysis is simplified with a software data analysis, thus offering the ability to quickly and reliably QC samples.

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TapeStation Automated Electrophoresis

This is an automated electrophoresis solution for the sample quality control of DNA and RNA samples. The system integrates an instrument, data processing software, reagents, and ScreenTape devices specific for DNA and RNA. It is suitable to analyze size, quantity, and integrity of samples, which is very effective for next-generation sequencing (NGS) or biobanking workflows.

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Pippin HT System

The Pippin systems from SageScience allow for precise automated size selection of nucleic acid samples, sequencing libraries, and even protein samples. Our core uses Pippin HT to enable high-throughput workflows to scale up sample preparation.

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Fast Real-Time PCR cycler

Real-Time PCR Thermal Cyclers/ Thermocyclers, also referred to as Quantitative PCR (qPCR), from Applied Biosystems calculate PCR amplification as it occurs. Relevant applications in our core include quantitative gene expression analysis, SNP analysis, drug target validation and genotyping.

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PCR working station

PCR Thermocyclers are instruments used to amplify DNA and RNA samples by the polymerase chain reaction. Amplified genetic material can be used in many downstream applications such as cloning, sequencing, expression analysis, and genotyping.

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Cold Storage

Cryogenic refrigerators ensure long-term storage of samples kept at cryogenic temperatures. Our core uses multiple monitoring systems to ensure temperature control storage for all samples received.

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Covaris focused-ultrasonicator

Covaris provides tools and technologies to improve pre-analytical sample preparation and it is suitable for continuous flow processing of biological and chemical applications including, crystallization and precipitation processes, chemical synthesis, cell lysis, and particle micronization.