Illumina NovaSeq 6000 Sequencing System
The NovaSeq 6000 is Illumina’s latest advancement in NGS sequencing instrumentation. The NovaSeq is a dual flow cell instrument that is engineered to operate with 3 patterned flow cell formats providing 0.5 Tb – 6 Tb of total sequence data output. The Genomics Core has upgraded the NovaSeq to perform the XP Chemistry upgrade for independent lane addressment. This scalable operation allows the Genomics Core to meet the demands of diverse sequencing projects from RNA-seq to Whole Genome Sequencing (WGS). The NovaSeq leverages Illumina’s proven Sequence by Synthesis (SBS) technology with superior run times and simplified RFID-encoded, cartridge based, reagent management for streamlined operation.
The patterned flow, cell first used on the HiSeq X system, has been adapted with improved density for the NovaSeq 6000. Each flow cell contains billions of nanowells in fixed locations producing even cluster spacing and uniform feature size to deliver extremely high cluster density. The high density afforded by the NovaSeq's patterned flow cell is combined with Illumina's proprietary onboard exclusion amplification clustering method (EXamp) which maximizes the nanowells that are occupied by DNA clusters originating from a single DNA template. This increased efficiency of flow cell utilization results in a significant increase in sequence data output.
10X Genomics Chromium Controller
The 10X Chromium Controller is a compact benchtop instrument that performs the encapsulation of individual cells or genomic DNA into 100K to 1M uniquely addressable partitions, each containing an identifying barcode for downstream genomic analysis. The Chromium Controller features a proprietary reagent delivery system that partitions disassociated cells or high molecular weight DNA molecules to process sequencing libraries for up to 8 samples in parallel. The partitioning process uses the 10X GemCode technology which delivers assay specific oligonucleotides into nanoliter-scale liquid/oil emusion partions for barcoding and amplification of targeted nucleic acid templates. The GemCode bead delivers up to ~4M available barcodes which provides an extremely high level of resolution for multiple applications. The Chromium Contoller performs the full suite of 10X Genomics applications.
Countess II Automated Cell Counter
Accurate cell counts and cell viability assessment is critical to the success of the Chromium Controller's operation. The Countess II Automated Cell Counter uses state-of-the-art optics and image analysis algorithms to analyze trypan blue stained cells in suspension. The Countess II allows for the rapid determination of cell concentration, cell viability and the presence of cell aggregates and contaminating debris in the cell suspension. This rapid quality control information allows the Genomics Core personal to properly adjust cell concentrations and perform remediations for clumping and contaminates which will ensure a successful run on the 10X Chromium Controller.
Additional equipment in support of the sequencing library preparation, validation and quantification includes the Covaris S2 Utrasonicator, Sage Science Pippin Prep preparative gel electrophoresis system, Agilent TapeStation 4200 and a Roche LightCycler96 Real Time PCR system.
The Covaris S2 Ultrasonicator allows for computer controlled fragmentation of nucleic acids using Adaptive Focused Acoustic (AFA) technology. Used to prepare fragmented genomic DNA with the appropriate size distribution for generating whole genome and ChIP sequencing libraries.
The Pippin Prep allows for automated electrophoretic size selection of fragmented DNA for sequencing library construction. Primarily used for library sizing of ChIP-seq and Small RNA library preparations.
The Agilent TapeStation 4200 provides a rapid assessment of fragment sizing using a ScreenTape based capillary electrophoresis system for independent sample quality control. Integrity assessment of total RNA is also performed on all samples prior to RNA-seq library preparation. Library validation and sizing is also a primary function for the TapeStation 4200.
The Roche LightCycler Real Time PCR system is used quantitate each sequence library preparation prior to sample pooling and sequencing. Real Time assays are performed using Roche FastStart Essential DNA Green Master Mix and KAPA Library Quant DNA Standards for Illumina sequencing. Accurate library concentrations allow the Genomics Core to tune the multiplexed sequencing strategies and obtain the targeted reads required to meet the needs of your project.