The Pacific Biosciences PacBio RS sequencing system will be used for high-throughput DNA sequencing in applications demanding long-range sequence information at the scale of tens of kilobases. The technology and characteristics of this sequencing technology are notably different than for other sequencing methodologies. In particular, the ability to obtain long sequence reads affords several critical advantages for a number of applications, including (1) the sequencing of novel genomes, (2) EST and transcriptome characterization in organisms lacking a sequenced or well-mapped genome, (3) the analysis of alternative pre-mRNA splicing, (4) amplicon sequencing. In addition to longer read lengths, the PacBio sequencing technology also provides rapid turnaround time. The PacBio RS will be applied to a diverse array of NIH-funded projects as well as other projects of high relevance to biomedical science, including the characterization of multigene families involved in sensory perception;the elucidation of the patterns and mechanisms of alternative pre-mRNA splicing;the characterization of genomes of genetic and evolutionary models of human development and disease;an analysis of the genetic loci associated with cancer;and an investigation of the susceptibility of mammalian cells to nutritional ions and environmental toxins. There are currently no PacBio sequencers on the UC Berkeley campus. The proposed instrument would be located close to its users as part of the Coates Genome Sequencing Center, and managed as part of the unified campus-wide sequencing core facility and associated Computational Genomics Resource Laboratory. Acquisition of this instrument will support researchers pursuing these projects, which promise to illuminate the fundamental mechanisms underlying human biology and disease.

Agency
National Institute of Health (NIH)
Institute
Office of The Director, National Institutes of Health (OD)
Type
Biomedical Research Support Shared Instrumentation Grants (S10)
Project #
1S10OD018174-01
Application #
8640752
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Birken, Steven
Project Start
2014-08-01
Project End
2015-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
1
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California Berkeley
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Brejc, Katjuša; Bian, Qian; Uzawa, Satoru et al. (2017) Dynamic Control of X Chromosome Conformation and Repression by a Histone H4K20 Demethylase. Cell 171:85-102.e23
McGlincy, Nicholas J; Ingolia, Nicholas T (2017) Transcriptome-wide measurement of translation by ribosome profiling. Methods 126:112-129
Inagaki, Soichi; Takahashi, Mayumi; Hosaka, Aoi et al. (2017) Gene-body chromatin modification dynamics mediate epigenome differentiation in Arabidopsis. EMBO J 36:970-980
Linck, Ethan B; Hanna, Zachary R; Sellas, Anna et al. (2017) Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens. Ecol Evol 7:4755-4767
Matsuo, Yoshitaka; Ikeuchi, Ken; Saeki, Yasushi et al. (2017) Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nat Commun 8:159
Knutson, Andrew Kek?pa'a; Egelhofer, Thea; Rechtsteiner, Andreas et al. (2017) Germ Granules Prevent Accumulation of Somatic Transcripts in the Adult Caenorhabditis elegans Germline. Genetics 206:163-178
Brooks, Brandon; Olm, Matthew R; Firek, Brian A et al. (2017) Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nat Commun 8:1814
Park, Dan M; Overton, K Wesley; Liou, Megan J et al. (2017) Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus. Mol Microbiol 104:46-64
Hosaka, Aoi; Saito, Raku; Takashima, Kazuya et al. (2017) Evolution of sequence-specific anti-silencing systems in Arabidopsis. Nat Commun 8:2161
Blair, John D; Hockemeyer, Dirk; Doudna, Jennifer A et al. (2017) Widespread Translational Remodeling during Human Neuronal Differentiation. Cell Rep 21:2005-2016

Showing the most recent 10 out of 19 publications