Genomics developing shared resource core
Mission
The mission of the Genomics developing shared resource core (launching June 2011) is to make available to VCU researchers the cutting-edge tools necessary for modern genomic analysis. As such, a primary focus of this core is on providing access to Next-Generation (NextGen) DNA sequencing and analysis capabilities.
Location and instrumentation
The laboratory is located on the fifth floor of Sanger Hall on the MCV campus. Commencing in June, 2011, the core laboratory offers will be able to offer services using the following suite of instrumentation:
Illumina HiSeq 2000
| Read Length | Single Flow Cell Run Time | Dual Flow Cell Run Time | Dual Flow Cell Output |
| 1 x 36 bp | ~ 1.5 days | ~ 2 days | 95-105 Gb |
| 2 x 50 bp |
~ 4.5 days | ~ 5.5 days | 270-300 Gb |
| 2 x 100 bp |
~ 8.5 days | ~ 11 days | 540-600 Gb |
Throughput |
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| Up to 55 Gb per day for a 2 x 100 bp run. | |||
Reads |
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| Up to three billion clusters passing filter and up to six billion paired-end reads | |||
Performance |
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| HiSeq Systems provide the greatest yield of perfect reads and bases greater than Q30 • Greater than 85% bases higher than Q30 at 2 x 50 bp • Greater than 80% bases higher than Q30 at 2 x 100 bp |
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Illumina Genome Analyzer IIx (GAIIx)
| Read Length | Run Time (Days) | Output (Gb) | |||
| 1 x 35 bp | ~2 | 10 - 12 | |||
| 2 x 50 bp | ~5 | 25 - 30 | |||
| 2 x 75 bp | ~7 | 37.5 - 45 |
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| 2 x 100 bp | ~9.5 | 54 - 60 | |||
| 2 x 150 bp | ~14 | 85 - 95 | |||
| *Sequencing output generated using TruSeq SBS V5 kit with PhiX library and cluster densities between 508,000-630,000 clusters/mm2 that pass filtering on a GAIIx | |||||
| Throughput | |||||
| Up to 6.5 Gb per day for a 2 x 100 bp run | |||||
| Reads | |||||
| Up to 320 million clusters passing filter and up to 640 million paired-end reads | |||||
| Performance | |||||
| The Genome AnalyzerIIx generates a significant yield of bases greater than Q30 •Greater than 85% bases higher than Q30 at 2 x 50 bp •Greater than 80% bases higher than Q30 at 2 x 100 bp |
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Roche 454 FLX (two machines)
| Throughput | 400-600 million high-quality, filter-passed bases per run* 1 billion bases per day |
| Run Time | 10 hours |
| Read Length | Average length = 400 bases |
| Accuracy | Q20 read length of 400 bases (99% at 400 bases and higher for prior bases) |
| Reads per run | >1 million high-quality reads |
| Data | Trace data accepted by NCBI since 2005 |
| Computing Requirements | Cluster recommended (Roche GS FLX Titanium Cluster available) |
| Robustness | No complex optics or lasers; reagents have long shelf life |
Contact information
For further information regarding the Genomics developing shared resource, please contact the director, Dr. Gregory Buck.
Gregory Buck, Ph.D.
resource director
(804) 828-2318
gabuck@vcu.edu
Citation
All publications that include results, services or products generated by VCU Massey Cancer Center Shared Resources must include the following acknowledgement in the manuscript:
"Services and products in support of the research project were generated by the VCU Massey Cancer Center Genomics Shared Resource, supported, in part, with funding from NIH-NCI Cancer Center Support Grant P30 CA016059."
