Virginia Commonwealth University

VCU Massey Cancer Center

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
Up to 55 Gb per day for a 2 x 100 bp run.

Reads
Up to three billion clusters passing filter and up to six billion paired-end reads

Performance
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

 

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
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

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."

PubMed Central (PMC) ID numbers are required for those publications that use CCSG-supported shared resources. All of Massey Cancer Center's shared resources are supported by the CCSG. Information to assist you with this process can be found here