Our group at the University of Tennessee Health Science Center (UTHSC) has just finished sequencing the genome of a strain of mouse that we use in phenotyping assays (strain DBA/2J from the Jackson Laboratory). We used SOLiD and Illumina (with Stan Nelson's group at UCLA) platforms. Much of the final SNP and indel data is already available on the GeneNetwork (GN) web site (www.genenetwork.org) in the SNP/Variant Browser.
We currently have two SOLiD systems (v 3.5) housed in our Molecular Resource Center. Eight groups of investigators at UTHSC are using the machines for a range of projects. Our own group (Williams/Lu/GeneNetwork) is interested in applying RNA-seq methods to expression QTL (eQTL) mapping and analysis (see GN site). It will be interesting to see if RNA-seq scales well to 100s of individuals. I sure hope so given our investment!
We currently have a good handle on whole genome shotgun sequencing, at least for mouse. RNA-seq is just coming on-line. We have experience with multiplex RNA-seq protocols (up to 12 samples so far, with ~25 million reads per sample per slide), but we have only taken the first steps in the analysis (Partek and export of files to UCSC Genome Browser).
St Jude Children's Research Hospital is another major research center in Memphis. They have approximately 12 Illumina GA systems on-site that they are using for a range of next gen projects and one massive cancer sequencing project (~1200 full genomes being sequenced). They also have a 454.
Happy to meet forum members and look forward to your input and help.
Robert W. Williams, Ph.D.
Director: Center for Integrative and Translational Genomics, UTHSC
Department of Anatomy and Neurobiology
[email protected]
We currently have two SOLiD systems (v 3.5) housed in our Molecular Resource Center. Eight groups of investigators at UTHSC are using the machines for a range of projects. Our own group (Williams/Lu/GeneNetwork) is interested in applying RNA-seq methods to expression QTL (eQTL) mapping and analysis (see GN site). It will be interesting to see if RNA-seq scales well to 100s of individuals. I sure hope so given our investment!
We currently have a good handle on whole genome shotgun sequencing, at least for mouse. RNA-seq is just coming on-line. We have experience with multiplex RNA-seq protocols (up to 12 samples so far, with ~25 million reads per sample per slide), but we have only taken the first steps in the analysis (Partek and export of files to UCSC Genome Browser).
St Jude Children's Research Hospital is another major research center in Memphis. They have approximately 12 Illumina GA systems on-site that they are using for a range of next gen projects and one massive cancer sequencing project (~1200 full genomes being sequenced). They also have a 454.
Happy to meet forum members and look forward to your input and help.
Robert W. Williams, Ph.D.
Director: Center for Integrative and Translational Genomics, UTHSC
Department of Anatomy and Neurobiology
[email protected]
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