Instruments
Genomic platform projects are enabled by a lineup of state-of-the-art liquid handling and measurement instruments that automate aspects of the sample preparation and sequencing process. Below is a list of our favorite instruments and short descriptions of their roles at CZ Biohub.
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10X Genomics Chromium Controller and Chromium X ControllerThe 10X microfluidic controllers capture thousands to hundreds of thousands of single cells or nuclei in droplets with barcoded oligos. These instruments are used for single cell RNA-seq, immune repertoire, chromatin accessibility and perturb-seq applications.
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Agilent Bravo Liquid HandlerThe Agilent Bravo is a compact and flexible automated liquid handling platform that transfers liquids and beads into 96 or 384 well plate formats. It has multiple deck options to convert manual pipetting protocols to automated ones.
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Agilent Fragment AnalyzerThe Fragment Analyzer is a capillary electrophoresis instrument for qualitative and quantitative analysis of DNA and RNA with a resolution of 3 base pairs. It can run 12 or 96 samples at a time for NGS sample prep or sequencing library QC for long or short read sequencing.
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Agilent TapestationThe Tapestation provides automated electrophoretic analysis of DNA and RNA for sample prep and QC of NGS library preps. This reliable and easy to use instrument can run nucleic acid samples in either 16-tube strips or 96-well microtiter plates.
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IntegraThe Integra Viaflo384 is an automated multichannel (96/384) pipetting robot used in our DNA extraction and Nextera library prep pipelines. It can be fitted with a 1 mL (96), 300 µL (96), and 12.5 µL (96 and 384) heads.
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ISeq 100iSeq is the smallest of Illumina sequencers that provides up to 4M reads. It is simple to setup and is used for rapid Covid sequencing at CZ Biohub. iSeq is also used to lightly sequence highly multiplexed libraries to check for evenness of pooling. One limitation iSeq has is that custom sequencing primers cannot be used.
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MantisMantis is an automated liquid dispenser that accurately dispenses volumes down to 100nL. The advantage is that the Mantis can dispense different volumes of the same solution into different wells of a 96/384 well plate. At CZ Biohub, we use the Mantis for DNA normalization and master mix reagent addition.
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MinIONMinION is a portable Nanopore sequencer used for long read sequencing. At CZ Biohub, it is primarily used to generate PCR free long reads for the purpose of generating genome assemblies or closing genomes of microbial organisms. It is also being developed to sequence full length cDNA from mammalian cells.
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Mission Bio TapestriThe Tapestri is a droplet microfluidic platform that captures single cells tagged with DNA bar coded antibodies and measures single nucleotide (SNPs) and copy number variants (CNV) from the same cell. This is the first commercial system to link phenotype (cell surface expression) with genotype in single cells.
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MiSeqMiSeq is one of the most accurate Illumina sequencers that provides up to 25M reads. MiSeq is the sequencer of choice for amplicons and/or libraries with low basepair diversity. At CZ Biohub, MiSeq is commonly used to sequence bacterial 16S libraries.
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MosquitoMosquito HTS is a high throughput liquid handler that allows rapid plate to plate low volume pipetting. At CZ Biohub, the Mosquito HTS is exclusively used with 384 well plates. The instrument uses positive displacement and can pipette volumes between 50 nL and 1.2 µL, which is ideal for our HTP Nextera XT library prep pipeline.
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NextSeq 500/550NextSeq is the first Illumina sequencer to use 2 color chemistry. It represents a good tradeoff between speed and throughput and is used for a variety of smaller scale projects at CZ Biohub. The rapid turnaround time also makes it ideal for ID-seq applications. NextSeq runs can provide up to 400M reads in 30 hours, and is available in mid and high outputs.
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NextSeq 2000NextSeq 2000 is the latest Illumina sequencer at CZ Biohub providing up to 1.1B reads per run. It features a super resolution optics system that uses a 2 color chemistry and patterned flow cells. Applications for NextSeq 2000 include single-cell RNA-seq, whole-exome sequencing, and small whole-genome sequencing.
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NovaSeq 6000NovaSeq is the highest throughput Illumina sequencer at CZ Biohub and provides up to 12B reads. It is also the most cost efficient way to generate Illumina sequencing reads. The NovaSeq uses 2 color chemistry and patterned flow cells. At CZ Biohub, it is used for a number of large scale projects including various cell atlases and microbiome studies.
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Sequel IIeSequel IIe is the latest single molecule PacBio sequencer, producing up to ~8 million reads per flow cell. At CZ Biohub, the Sequel IIe is used in various projects requiring longer reads, such as full length antibody repertoire sequencing. It is also used to sequence PCR free genomic DNA when assembly is required for eukaryotic organisms.
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Sony SH800S Fluorescence Activated Cell SorterSony FACS sorts cells using novel microfluidic sorting chips for multiple cell sizes (70, 100,130 uM). It has four excitation lasers (488, 405, 561 and 638nm) and six fluorescence detectors. It is easy to maintain, align and acquire cells to sort into tubes and 96 and 384 well plates.
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SPT labtech Dragonfly Discovery Liquid DispenserThe Dragonfly is a broad range liquid volume dispenser useful for low volume master mix into 96, 384 or 1536 well plate formats. It is reliable and easy to use with a single syringe and tip type that works accurately with all types of liquids and beads.
