27 research outputs found
Bean Dance: the Hopi Tradition
This book was completed for Jan Baker\u27s artists\u27 book class.https://digitalcommons.risd.edu/specialcollections_bookmark_senses/1012/thumbnail.jp
Land of Enchantment
This book was completed for Jan Baker\u27s artists\u27 book class, Printed Books.https://digitalcommons.risd.edu/specialcollections_bookmark_senses/1011/thumbnail.jp
Finishing the euchromatic sequence of the human genome
The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead
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The complete sequence of human chromosome 5
Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-encoding genes including the protocadherin and interleukin gene families and the first complete versions of each of the large chromosome 5 specific internal duplications. These duplications are very recent evolutionary events and play a likely mechanistic role, since deletions of these regions are the cause of debilitating disorders including spinal muscular atrophy (SMA)
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Automated High-Throughput Fosmid Isolation and End-Sequencing Using Magnetic Beads and Reduced Terminator Cycling Sequencing Reaction Kit
Automated High-Throughput Fosmid Isolation and End-Sequencing Using Magnetic Beads and Reduced Terminator Cycling Sequencing Reaction Kit
Five page letter from Fayez Sayegh to Robert C. North, Department of Political Science, Stanford University, May 1, 1960, expressing his anxiety about the lengthy, involved process of having his visiting professorship approved by the University
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Pyrosequencing Strategies for cDNA Libraries
The US DOE Joint Genome Institute (JGI) is a high-throughput genomics facility involved in sequencing a variety of organisms. A major effort at JGI is the sequencing of genomes and microbial community samples of relevance to the DOE missions of carbon sequestration, bioremediation and energy production. cDNA/EST sequencing is an integral part of genomic sequencing because it provides crucial information for gene models and genome annotation. The 454 sequencing platform is an integrated system of emulsion-based PCR amplification of hundreds of thousands of DNA fragments linked to high throughput parallel pyrosequencing in picoliter-sized wells. Several strategies have been designed and carried out at JGI to use the 454 platform for cDNA/EST sequencing. cDNA libraries constructed by conventional methods were subjected to direct 454 sequencing. In addition, special primers and adaptors were also designed for library construction so the directional sequencing feature of the 454 technology can be used to sequence a particular end of the cDNA/EST fragments. Adaptor sequences used by 454 library construction can be incorporated into polyT primer, cap primer and/or random primer for cDNA/EST library construction. The 454 sequencing platform can deliver 200 to 400 thousand cDNA/EST reads from a single run and does not require cloning step, potentially improving the coverage obtained through traditional Sanger sequencing. The large numbers of short reads generated by the 454 platform can be aligned to genome assemblies to extend and confirm gene models. Results from different strategies of library construction combined with 454 sequencing will be presented. The coverage of the library and the novelty rate are compared with traditional Sanger sequencing. The possible assembly problems caused by short reads with slightly higher error rate from 454 will also be addressed
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Combining 454 Sequencing and Traditional Sanger Reads for Microbial Genomes
The US DOE Joint Genome Institute (JGI) is a high-throughput sequencing center involved in a myriad of sequencing projects. A major effort at JGI is the sequencing of microbial genomes of relevance to the DOE missions of carbon sequestration, bioremediation and energy production. The JGI Microbial Program is responsible for the generation of over 200 microbial genomes and we are interested in utilizing new technologies to increase capacity. The 454 sequencing platform is an integrated system of emulsion-based PCR amplification of hundreds of thousands of DNA fragments linked to high throughput parallel pyrosequencing in picoliter-sized wells. The 454 sequencing platform can deliver 30 to 50 million base pairs (mbp) from a single run, however, our previous study revealed that the quality of the resulting assembly contains high numbers of misassemblies and base errors due to short read length and lack of paired-end information. The traditional Sanger sequencing method is lower in throughput and more costly but it provides high quality sequencing results and more accurate assemblies. The paired-end information from Sanger sequencing is proven to be crucial in scaffolding and gap closure. We combined 454 sequencing results with different amounts of paired Sanger sequencing reads from three different sized shotgun libraries and analyzed the results. Assemblies from all combinations were done by Newbler and Phred/Phrap and viewed and analyzed by Consed and in-house developed software. Numbers of remaining gaps and low quality regions from different combinations were assessed. Distribution of coverage and possible errors were analyzed for both platforms. We will also discuss the optimal ratio of data from 454 and Sanger sequencing to achieve high quality finished microbial genome sequences in a time and cost effective manner
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Implementing the Agencourt SprintPrep384 Protocol at JGI
Implementing the Agencourt SprintPrep384 Protocol at JGIPresenting Author: Steven E. Wilson Contributing Authors: Paul Richardson, Feng Chen, Jamie Jett, Nancy Hammon, Duane Kubischta, Diana Lawrence U.S. DOE Joint Genome Institute 2800 Mitchell Drive, Bldg. 100 Walnut Creek, CA 94598 [email protected](925) 296-5769 SprintPrep DNA isolation is a process that allows large fragments of DNA and vectors to be isolated from the host E. Coli cell. Agencourt has developed SprintPrep reagents and semi-automated methods for performing the necessary protocol. Last year, JGI implemented a 96 well SprintPrep method. This year, JGI has made the 384 SprintPrep method virtually user-independent. Moving from the 96 well fosmid isolation method to the 384 well format has led to cost savings due to reagent reductions and a doubling in sequencing throughput. The increase in throughput will lead to an increase in sequencing depth and data confidence