{"@context":"http://iiif.io/api/presentation/2/context.json","@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/manifest.json","@type":"sc:Manifest","label":"Improved Methodology of DNA Fragmentation using Micro-patterned PDMS Stamps to Apply Cutting Enzymes","metadata":[{"label":"dc.description.sponsorship","value":"This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree."},{"label":"dc.format","value":"Monograph"},{"label":"dc.format.medium","value":"Electronic Resource"},{"label":"dc.identifier.uri","value":"http://hdl.handle.net/11401/78274"},{"label":"dc.language.iso","value":"en_US"},{"label":"dcterms.abstract","value":"The development of sequencing since the Human Genome Project has greatly advanced. Current Next Generation Sequencing (NGS) platforms can produce more cost-effective sequencing in a shorter amount of time by using massively parallel sequencers. However, current NGS platforms have limitations in that only DNA fragments of size 100-300 bases may be analyzed. When producing these fragments of DNA, the positional order is often lost due to random fragmentation. Additionally, with repeats, insertions, and deletions of the genome, it further complicates the construction of contigs. Although companies such as Pacific Biosciences have developed longer-read technologies which sequences longer fragments (10 kilobases), the contig assembly problem remains for complex genomes. In this study, a newly developed method of fragmenting DNA that maintains the order is used. The method involves coating the surface of a soft lithography Poly dimethylsiloxane (PDMS) stamp with Dnase I enzyme. The stamp was placed onto a Poly (methyl methacrylate) \u2013 coated silicon wafer that has stretched linearized DNA on the surface, thereby inducing fragmentation in a controlled manner. The previously used methods of coating the PDMS with Dnase I enzymes often had inconsistent coatings because it was manually applied. Experiments were conducted utilizing a PDMS stamp having micron-sized microwells dipped into and withdrawn from a DNase I enzyme solution using a computer-controlled stepping motor and linear stage. Through surface tension, this method allowed the DNase I enzyme to remain in the microwells. Thereafter, using fluorescence microscopy, it was demonstrated that the DNase I enzyme was deposited in the microwells and had successfully cut at the desired locations."},{"label":"dcterms.available","value":"2018-06-21T13:38:50Z"},{"label":"dcterms.contributor","value":"Meng, Yizhi"},{"label":"dcterms.creator","value":"Liu, Donald"},{"label":"dcterms.dateAccepted","value":"2018-06-21T13:38:50Z"},{"label":"dcterms.dateSubmitted","value":"2018-06-21T13:38:50Z"},{"label":"dcterms.description","value":"Department of Materials Science and Engineering"},{"label":"dcterms.extent","value":"48 pg."},{"label":"dcterms.format","value":"Monograph"},{"label":"dcterms.identifier","value":"http://hdl.handle.net/11401/78274"},{"label":"dcterms.issued","value":"2017-12-01"},{"label":"dcterms.language","value":"en_US"},{"label":"dcterms.provenance","value":"Made available in DSpace on 2018-06-21T13:38:50Z (GMT). No. of bitstreams: 1\nLiu_grad.sunysb_0771M_13577.pdf: 4125875 bytes, checksum: 1977c536428ae2fc41ead500023db2ee (MD5)\n  Previous issue date:   12"},{"label":"dcterms.subject","value":"Next Generation Sequencing"},{"label":"dcterms.title","value":"Improved Methodology of DNA Fragmentation using Micro-patterned PDMS Stamps to Apply Cutting Enzymes"},{"label":"dcterms.type","value":"Thesis"},{"label":"dc.type","value":"Thesis"}],"description":"This manifest was generated dynamically","viewingDirection":"left-to-right","sequences":[{"@type":"sc:Sequence","canvases":[{"@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/canvas/page-1.json","@type":"sc:Canvas","label":"Page 1","height":1650,"width":1275,"images":[{"@type":"oa:Annotation","motivation":"sc:painting","resource":{"@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/79%2F63%2F18%2F79631887860863175411739925173371418170/full/full/0/default.jpg","@type":"dctypes:Image","format":"image/jpeg","height":1650,"width":1275,"service":{"@context":"http://iiif.io/api/image/2/context.json","@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/79%2F63%2F18%2F79631887860863175411739925173371418170","profile":"http://iiif.io/api/image/2/level2.json"}},"on":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/canvas/page-1.json"}]}]}]}