General Information
Facility Description
Laboratory facilities include instruments from the Office of the Vice President of Research’s Georgia Genomics Facility. The combined lab space includes separate pre- and post-PCR laboratories (800 and 3200 sq. ft. respectively) are in the Riverbend North lab complex on the UGA campus in Athens.
The Pre-PCR labs include: a Hydra 96-well pipetter, fume hood, refrigerators, freezers, ultra-cold freezers, centrifuges, balances and other small equipment needed for DNA extraction and setting up PCR reactions. Dedicated pre-PCR equipment for the preparation of 454 libraries and emPCRs include a Covarus S2, Agilent BioAnalyzer 2000, Qiagen Tissuelyzer, and an epMotion pipetting system.
The post-PCR labs include: Applied Biosystems 3730xl, and two 3100 capillary genetic analyzers for DNA sequencing and genotyping; a Roche Lightcycler 480 Thermal Cycler and Applied Biosystems OpenArray for Real-Time PCR and low-throughput SNP detection; Illumina BeadXpress for high-throughput SNP genotyping; 2 Hydra 96-well pipetters; 5 Applied Biosystems 9700 thermocyclers (3 dual 96-well, and 2 dual 384-well); Shimatzu MultiNA; epMotion pipetting system; refrigerators, freezers, and ultra-cold freezers; electronic balances and pH meters; NanoDrop 2000 and fluorometers; micro-, electronic, and multichannel pipetters; agarose and acrylamide gel rigs; various centrifuges; incubators for bacterial cloning and DNA hybridization; and Macintosh and PC computers loaded with DNA sequence analysis software (e.g., Sequencher, Arlequin, PAUP* 4.0, etc.). Dedicated post-PCR equipment for the preparation of 454 sequences include a 454 GS FLX system, Beckman Coulter Z2 bead counter, and Beckman Coulter Allegra X-15R centrifuge.
In-house bioinformatic resources for the analysis of 454 sequences consist of a dedicated 5 node (20-core, 32 GB RAM) RedHat computer cluster for base-calling and assembly of 454 data directly from the 454 GS FLX, and an 8-core MacPro with 32 GB RAM dedicated to the post analysis of 454 sequencing data. Available core data pipelines include Newbler, MIRA, PHRAP, etc. for assembly, and Python for post assembly processing. Additional computational resources (5 RedHat clusters - totaling 513 nodes, 1644 processor cores and 3288 GB RAM) are available from the UGA core Research Computing Center and the Institute of Bioinformatics.
All offices are equipped with networked personal computers. Administrative and secretarial support personnel assist with purchasing, property management, record keeping, billing, etc.
