Instrumentation and facilities
EnGGen hosts instrumentation for most modern genetic or genomic investigations. Some instruments are available for use at no cost while others have an associated per-usage cost.
Illumina sequencing Accordion Closed
An Illumina MiSeq is available for use at EnGGen. Users submit samples and EnGGen staff operate the sequencer. A MiSeq run generates between 10-25 million sequences per run in 25-300 base read lengths depending on the selected run mode. Sequencing can be performed in single direction or paired-end configurations. Overlapping paired-end reads can easily be joined for end-user analysis.
Sanger sequencing Accordion Closed
An Applied Biosystems 3730xl (96 capillary) sequencer is available in EnGGen. The 3730 is configured with a 50cm column for increased sequencing read length, and is ideal for large-scale production of targeted resequencing projects or various fragment analysis applications (e.g. microsatellites or AFLP).
Standard thermal cyclers Accordion Closed
EnGGen has 2 Applied Biosystems Veriti cyclers, 4 BioRad iCyclers and an MJ PTC200 available for use with 96-well format assays. A BioRad Tetrad2 with four blocks and 2 Applied Biosystems Veriti cyclers are equipped with 384 well blocks. 96-well blocks offer gradient cycling for use in protocol optimization.
Real-Time PCR instruments Accordion Closed
An Applied Biosystems QuantStudio5 (384 well) is available for real-time and quantitative PCR assays. Each cycler offers fully-featured and customizable protocols, multi-channel detection, and integrated analysis software.
Fragment Analyzer Accordion Closed
An AATI Fragment Analyzer is available for use. Fragment Analyzer data provides quantitative results detailing the amount and size of DNA or RNA present in a sample. This is useful for assessing the quality of a library intended for Illumina sequencing or for checking the quality of an RNA extract prior to embarking on downstream steps.
Pippin Prep Accordion Closed
A Pippin Prep from Sage Science is available for highly accurate size selection. This is especially useful for preparing samples intended for genome assembly or for high throughput genotyping assays employing reduced representation libraries.
Automated liquid handler Accordion Closed
EnGGen utilizes a Packard MultiProbe II Plus HT EX automated liquid handling system. It provides an efficient and accurate way to perform reaction setup, normalize DNA samples, and pool amplicon products for Illumina sequencing.
Tissue disruption Accordion Closed
A Spex MiniG 1600 is available for homogenizing various tissues in various sized tubes or plates. When used with appropriate grinding material (e.g. glass or steel beads), most tissues will be homogenized within one to a few minutes.
DNA quantification Accordion Closed
Two NanoDrop spectrophotometers are available for absorbance-based quantification of individual samples (DNA, RNA, protein). A Hoefer Dyna Quant 300 fluorometer is also available for fluorescence-based quantification of dsDNA. For high-throughput needs, a BioTek Synergy HTX plate reader is available which can read many samples simultaneously for absorbance or fluorescence-based assays (excitation filters: 360/40, 485/20; emission filters: 460/40, 528/20).
Bench space Accordion Closed
Bench space is available at EnGGen for sample processing. Each bench has adequate space, storage shelves, a pipette set, a vortexer, and a heated dry bath. Ancillary equipment such as centrifuges, multichannel pipettes, electronic pipettes, and a PCR set up hood are also available.
Bioinformatic processing Accordion Closed
Linux and Windows-based computer workstations are available in EnGGen. A wide range of software platforms are available, including Geneious (comprehensive genomics suite), GeneMarker (fragment analysis suite), Staden Package (sequence data analysis), BioEdit (sequence data analysis), MEGA (phylogenetics analysis), and QIIME (microbial community analysis).