Instrumentation

EnGGen equipment and testing materials

Available instrumentation 

EnGGen hosts adequate instrumentation for most modern genetic or genomic investigations.  Some instruments, such as thermal cyclers, are available for use at no cost.  Others, such as DNA sequencers, have an associated per-usage cost.  Instrument use can be scheduled through our resources calendar at LabAgenda (requires an invitation to our group in order to participate).

Illumina sequencing
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
Applied Biosystems 3730xl (96 capillary) and 3130 (4 capillary) sequencers are 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).  The 3130 has a 36cm column and is perfect for optimizing protocols for projects before committing to the higher up-front cost of the 3730.
Standard thermal cyclers
EnGGen has 4 BioRad iCyclers, an MJ PTC200, and 2 Applied Biosystems Veriti cyclers 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.
Quantitative thermal cyclers
An Applied Biosystems QuantStudio5 (384 well), a BioRad iCycler (96 well) with IQ5 head and an Eppendorf Realplex4 (96 well) are all available for qPCR assays.  Each cycler features customizable protocols, multi-channel detection, melt curve analysis, and integrated analysis software.
Bioanalyzer
An Agilent Bioanalyzer 2100 is available for use.  Bioanalyzer data give quantitative results which detail 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
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 such as RADseq.
Automated liquid handler
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
A Spex MiniG 1600 is available for homogenizing various tissues.  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
Two Nanodrop spectrophotometers are available for absorbance-based quantification of individual samples (DNA, RNA, protein).  A Hoefer Dynaquant 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.
Clean bench space
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
Linux and Windows-based computer workstations are available in EnGGen.  Numerous software is 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).  Additionally, EnGGen staff are knowledgeable about how to migrate your data to the local compute cluster (monsoon) for increased processing power.