Ordered Restriction Maps of
            <i>Saccharomyces cerevisiae</i>
            Chromosomes Constructed by Optical Mapping

Schwartz, David C.; Li, Xiaojun; Hernández, Leticia; Ramnarain, Satyadarshan P.; Huff, Edward J.; Wang, Yu-Ker

doi:10.1126/science.8211116

Cited by 398 publications

(313 citation statements)

References 22 publications

Supporting

Mentioning

308

Contrasting

Unclassified

Order By: Relevance

“…High molecular weight DNA was obtained from Chinese hamster tissues. Whole genome shotgun, single-molecule restriction maps were generated using the automated Argus system (OpGen Inc., Maryland, USA), based on the optical mapping technology 51,52 . Individual DNA molecules were deposited onto silane-derivatized glass surfaces in MapCards (OpGen Inc., MD, USA) and digested by BamHI enzyme.…”

Section: Methodsmentioning

confidence: 99%

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Lewis¹,

et al. 2013

View full text Add to dashboard Cite

Chinese hamster ovary (CHO) cells, first isolated in 1957, are the preferred production host for many therapeutic proteins. Although genetic heterogeneity among CHO cell lines has been well documented, a systematic, nucleotide-resolution characterization of their genotypic differences has been stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages. This analysis identified hamster genes missing in different CHO cell lines, and detected >3.7 million single-nucleotide polymorphisms (SNPs), 551,240 indels and 7,063 copy number variations. Many mutations are located in genes with functions relevant to bioprocessing, such as apoptosis. The details of this genetic diversity highlight the value of the hamster genome as the reference upon which CHO cells can be studied and engineered for protein production.

show abstract

Section: Methodsmentioning

confidence: 99%

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Lewis¹,

et al. 2013

View full text Add to dashboard Cite

show abstract

“…We return at this point to a comparison of our method to that of Schwartz et al (5,6). These authors have achieved a resolution of 1.1 kbp using 20-150 molecules (20).…”

Section: [1]mentioning

confidence: 98%

“…To date, the most powerful method for constructing restriction maps of long DNA molecules (100 kbp and above) is the one developed by Schwartz and coworkers (5,6). Their technique consists of stretching the DNA on a surface to establish a one-to-one mapping between spatial and genomic position, initiating the restriction by exposing the DNA to restriction enzymes and Mg 2ϩ , and optically observing the lengths of the resulting fragments.…”

mentioning

confidence: 99%

Restriction mapping in nanofluidic devices

Riehn

Wang

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

191

183

View full text Add to dashboard Cite

We have performed restriction mapping of DNA molecules using restriction endonucleases in nanochannels with diameters of 100 -200 nm. The location of the restriction reaction within the device is controlled by electrophoresis and diffusion of Mg 2؉ and EDTA. We have successfully used the restriction enzymes SmaI, SacI, and PacI, and have been able to measure the positions of restriction sites with a precision of Ϸ1.5 kbp in 1 min using single DNA molecules.R estriction mapping with endonucleases is a central method in molecular biology (1, 2). It is based on the measurement of fragment lengths after digestion, while possibly maintaining the respective order. We present here an approach to restriction mapping that is based on stretching DNA in nanofluidic channels, in which DNA is linearized to a length-independent fraction of its contour length (3, 4).To date, the most powerful method for constructing restriction maps of long DNA molecules (100 kbp and above) is the one developed by Schwartz and coworkers (5, 6). Their technique consists of stretching the DNA on a surface to establish a one-to-one mapping between spatial and genomic position, initiating the restriction by exposing the DNA to restriction enzymes and Mg 2ϩ , and optically observing the lengths of the resulting fragments. An elegant study of the same basic approach showing separation of specific binding and induced cutting was published by Taylor et al. (7).A fundamental principle in determining the error of a measurement, and a common strategy to reduce the experimental error, is to take multiple, statistically independent measurements of the same quantity. Note that the fixing of the molecule to the surface in Schwartz's approach prevents any fluctuations, and hence multiple molecules have to be observed to obtain statistically independent measurements of the same cut position. Moreover, genomic-length DNA molecules stretched on surfaces often exhibit inhomogeneous stretching, including breaks, and thus averaging over multiple molecules becomes imperative (6,8). In contrast, a molecule stretched inside a nanochannel is not subject to any forces other than those causing lateral confinement and thus is able to thermally relax and fluctuate around an equilibrium conformation. The evaluation of a single molecule is thus sufficient if complete digestion is achieved. A detailed description of the statistics and dynamics of DNA molecules in nanochannels is published in ref. 9.The main challenge in employing the concept of stretching and mapping DNA inside a closed fluidic system is to separate the steps of stretching and cutting. We have solved this problem by introducing the DNA electrophoretically into nanochannels and controlling the concentration of the enzyme cofactor Mg 2ϩ in the device shown in Fig. 1. It consists of a microfluidic ''loading'' channel containing the DNA to be analyzed, the restriction enzyme, and EDTA, and a microfluidic ''exit'' channel containing Mg 2ϩ and the restriction enzyme. The two microfluidic channels are linked by 10 n...

show abstract

“…There are several examples in the literature that demonstrate that the distributions of many molecular properties, as determined by SMD techniques, are Gaussian (14 -21). Likewise, there are studies that report molecular property measurements based on fewer than 10 measurements (22)(23)(24)(25). However, these studies do not present a statistical analysis of the sample size or a detailed discussion to support the limited sample size relative to experimental parameters.…”

mentioning

confidence: 99%

Statistics of single‐molecule measurements: Applications in flow‐cytometry sizing of DNA fragments

Ferris¹,

Habbersett²,

Wolinsky³

et al. 2004

Cytometry Pt A

View full text Add to dashboard Cite

Background:The measurement of physical properties from single molecules has been demonstrated. However, the majority of single-molecule studies report values based on relatively large data sets (e.g., N Ͼ 50). While there are studies that report physical quantities based on small sample sets, there has not been a detailed statistical analysis relating sample size to the reliability of derived parameters. Methods: Monte Carlo simulations and multinomial analysis, dependent on quantifiable experimental parameters, were used to determine the minimum number of singlemolecule measurements required to produce an accurate estimate of a population mean. Simulation results were applied to the fluorescence-based sizing of DNA fragments by ultrasensitive flow cytometry (FCM). Results: Our simulations show, for an analytical technique with a 10% CV, that the average of as few as five

show abstract

Ordered Restriction Maps of Saccharomyces cerevisiae Chromosomes Constructed by Optical Mapping

Cited by 398 publications

References 22 publications

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Restriction mapping in nanofluidic devices

Statistics of single‐molecule measurements: Applications in flow‐cytometry sizing of DNA fragments

Contact Info

Product

Resources

About