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77-459: As the former Perkin-Elmer, Applera had a history dating back to 1931. But more precisely, its history dates from 1999, when Perkin-Elmer effectively split in half, and sold off its more traditional half of the business to EG&G Inc. As part of the deal, it also sold the Perkin-Elmer name, because that most properly associated with that traditional line of products, and EG&G then became

154-405: A laser beam of a defined wavelength. Relative intensities of each fluorophore may then be used in ratio-based analysis to identify up-regulated and down-regulated genes. Oligonucleotide microarrays often carry control probes designed to hybridize with RNA spike-ins . The degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements for

231-517: A combination of its two components' names, Appl era . The Applera Corporation Directors oversaw the parent corporation along with the operations of both tracking stock groups, and consequently they had the responsibility of fairly balancing the interests of both groups of investors in each stock. The original Perkin-Elmer, and then its successor PE Corporation and Applera Corporation have been headquartered in Norwalk, Connecticut. The company address

308-661: A cost of only US$ 200 million, about 1/10 of the consortium projected cost of US$ 3 billion. However, it would mean starting from scratch, eight years already into the consortium's program. It was a bold prediction, given that the consortium target date set by Watson back in 1990 had been the forward year of 2005, only seven years away, and with the consortium already half the way to the completion target date by then. Also, it meant that Hunkapiller's idea would require competing against his own customers, to all of whom Applied Biosystems sold its sequencing machines and their chemical reagents. However, he calculated that it would also mean doubling

385-425: A fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and Cy 5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum). The two Cy-labeled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores after excitation with

462-501: A joint venture with Raytheon Technical Services , creating JT3 LLC in 2000, which operates the Joint Range Technical Services contract. EG&G Technical Services, Inc. and Lear Siegler Services, Inc. consolidated, becoming one of the nation's leading U.S. federal government contractors providing operations and maintenance, systems engineering and technical assistance, and program management, primarily to

539-588: A key equipment maker, Applied Biosystems , Inc., and that stock's symbol ABIO ceased trading on the NASDAQ exchange, as it became a division of Perkin-Elmer. Michael W. Hunkapiller, Ph.D., who had been Applied Biosystem's chairman, president and CEO since 1983, became a senior vice president of Perkin-Elmer, and president of the Applied and PE Biosystems Divisions. In 1994, Perkin-Elmer reported net revenues of over $ 1 billion, of which Life Sciences accounted for 42% of

616-404: A leader in the bio-instrumentation field where it made biomolecule purification systems for protein analysis. Noubar Afeyan , Ph.D., had been the founder, chairman, and CEO of PerSeptive, and after the acquisition he became a senior vice president and chief business officer of Perkin-Elmer. He had earlier founded and co-built several successful life science and technology startup companies through

693-409: A nucleotide sequence means tighter non-covalent bonding between the two strands. After washing off non-specific bonding sequences, only strongly paired strands will remain hybridized. Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions (such as temperature), and washing after hybridization. Total strength of the signal, from

770-476: A presence on the World Wide Web at http://www.perkin-elmer.com . While planning the next new generation of machines, PE Biosystems' president, Michael W. Hunkapiller, calculated that it would be possible for their own private industry to decode the human genome before the academic consortium could complete it. The company would decode all of the 3.5 billion chemical letters in the human DNA by 2001, at

847-413: A spot (feature), depends upon the amount of target sample binding to the probes present on that spot. Microarrays use relative quantitation in which the intensity of a feature is compared to the intensity of the same feature under a different condition, and the identity of the feature is known by its position. Many types of arrays exist and the broadest distinction is whether they are spatially arranged on

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924-496: A surface or on coded beads: DNA microarrays can be used to detect DNA (as in comparative genomic hybridization ), or detect RNA (most commonly as cDNA after reverse transcription ) that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling . Applications include: Specialised arrays tailored to particular crops are becoming increasingly popular in molecular breeding applications. In

1001-782: A time across the entire array. Each applicable probe is selectively "unmasked" prior to bathing the array in a solution of a single nucleotide, then a masking reaction takes place and the next set of probes are unmasked in preparation for a different nucleotide exposure. After many repetitions, the sequences of every probe become fully constructed. More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes. Two-color microarrays or two-channel microarrays are typically hybridized with cDNA prepared from two samples to be compared (e.g. diseased tissue versus healthy tissue) and that are labeled with two different fluorophores . Fluorescent dyes commonly used for cDNA labeling include Cy 3, which has

1078-435: A variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing, or electrochemistry on microelectrode arrays. In spotted microarrays , the probes are oligonucleotides , cDNA or small fragments of PCR products that correspond to mRNAs . The probes are synthesized prior to deposition on

1155-419: Is at 50 Danbury Rd. In the early 1990s, Perkin-Elmer, which had been a maker of diverse electronic instruments and analytical and optical equipment, established strong ties with groups closely involved with the business of decoding the human genome . By the late 1990s, Perkin-Elmer's Life Sciences division had become centrally involved in highly publicized intense competition against the public consortium that

1232-497: Is being conducted by the US Food and Drug Administration (FDA) to develop standards and quality control metrics which will eventually allow the use of MicroArray data in drug discovery, clinical practice and regulatory decision-making. The MGED Society has developed standards for the representation of gene expression experiment results and relevant annotations. Microarray data sets are commonly very large, and analytical precision

1309-427: Is difficult to exchange due to the lack of standardization in platform fabrication, assay protocols, and analysis methods. This presents an interoperability problem in bioinformatics . Various grass-roots open-source projects are trying to ease the exchange and analysis of data produced with non-proprietary chips: For example, the "Minimum Information About a Microarray Experiment" ( MIAME ) checklist helps define

1386-406: Is expected to detect is not trivial. Some mRNAs may cross-hybridize probes in the array that are supposed to detect another mRNA. In addition, mRNAs may experience amplification bias that is sequence or molecule-specific. Thirdly, probes that are designed to detect the mRNA of a particular gene may be relying on genomic EST information that is incorrectly associated with that gene. Microarray data

1463-549: Is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and the measurement of gene expression. The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs . A high number of complementary base pairs in

1540-419: Is influenced by a number of variables. Statistical challenges include taking into account effects of background noise and appropriate normalization of the data. Normalization methods may be suited to specific platforms and, in the case of commercial platforms, the analysis may be proprietary. Algorithms that affect statistical analysis include: Microarray data may require further processing aimed at reducing

1617-414: Is used by research scientists around the world to produce "in-house" printed microarrays in their own labs. These arrays may be easily customized for each experiment, because researchers can choose the probes and printing locations on the arrays, synthesize the probes in their own lab (or collaborating facility), and spot the arrays. They can then generate their own labeled samples for hybridization, hybridize

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1694-416: Is usually detected and quantified by detection of fluorophore -, silver-, or chemiluminescence -labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown . An example of its application

1771-516: The Cold war era (from 1948 and onward). It had close involvement with some of the government's most sensitive technologies. In 1931, Massachusetts Institute of Technology (MIT) professor Harold Edgerton , a pioneer of high-speed photography , partnered with his graduate student Kenneth Germeshausen to found a small technical consulting firm. The two were joined by fellow MIT graduate student Herbert E. Grier in 1934. Bernard "Barney" O'Keefe became

1848-810: The New York Stock Exchange , to great excitement. On May 28, 1999, as part of the recapitalization and reorganization, the company completed the sale of its traditional business unit, the Analytical Instruments Division to EG&G Inc., along with the Perkin-Elmer name, for US$ 425 million. EG&G was based in Wellesley, Massachusetts , and made products for diverse industries including automotive, medical, aerospace and photography. On July 14, 1999, that new analytical instruments maker PerkinElmer cut 350 jobs, or 12%, in its cost reduction reorganization. On June 17, 1999,

1925-464: The expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles (10 moles ) of a specific DNA sequence, known as probes (or reporters or oligos ). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called target ) under high-stringency conditions. Probe-target hybridization

2002-754: The 1950s and 1960s, EG&G was involved in nuclear tests as a major contractor for the Atomic Energy Commission . EG&G made extensive use of the Nevada Test Site (NTS) for weapons development and high-technology military testing at Nellis AFB . EG&G has shared operations responsibility for the NTS with Livermore Labs , Raytheon Services Nevada , Reynolds Electrical and Engineering (REECO) and others. Subsequently, EG&G expanded its range of services, providing facilities management, technical services, security, and pilot training for

2079-432: The 1970s and 1980s, the company, then led by O'Keefe, diversified by acquisition into the fields of paper making, instrumentation for scientific, marine, environmental and geophysical users, automotive testing, fans and blowers, frequency control devices and other components including BBD and CCD technology via their Reticon division. In the late 1980s and early 1990s most of these divisions were sold, and on 28 May 1999,

2156-609: The 1990s, after earning his Ph.D. in biochemical engineering from the Massachusetts Institute of Technology in 1987. In 1998, Perkin-Elmer formed the PE Biosystems division, by consolidating Applied Biosystems, PerSeptive Biosystems, Tropix and PE Informatics. Informatics was formed from the Perkin-Elmer combination of two other acquisitions, Molecular Informatics and Nelson Analytical Systems, with existing units of Perkin-Elmer. By 1998, Perkin-Elmer had

2233-558: The Departments of Defense and Homeland Security. The companies are separate legal entities, but share a common management. In December 2009, URS announced its decision to discontinue the Lear Siegler name for this division. DNA chip A DNA microarray (also commonly known as DNA chip or biochip ) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure

2310-521: The EG&;G name and logo. In the same press release, URS stated that it would also retire two other acquired brands, Washington Group and Lear Siegler. URS Chief Executive Officer Martin Koffel explained the change in an e-mail transmitted to employees: "In today's marketplace, it is essential we present a consistent, unified brand to our customers and achieve the competitive advantages enjoyed by our peers in

2387-545: The Group in 2003, replaced him as president of Applied Biosystems Group. EG%26G EG&G , formally known as Edgerton, Germeshausen, and Grier , Inc., was a United States national defense contractor and provider of management and technical services. The company was involved in contracting services to the United States government during World War II and conducted weapons research and development during

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2464-452: The June fiscal year end, which would be its first profitable year. But it had always faced the problem that its public competitor, the consortium project, provides free data from its own database. In 2002, Applied Biosystems Group again posted revenues of US$ 1.6 billion for the year. In 2004, the long-term Applied Biosystems president, Mike Hunkapiller, retired and Cathy Burzik, who had joined

2541-581: The PE Biosystems Group's sales reached US$ 940 million. Its chief new genomics instrument was the ABI PRISM 3700 DNA Analyzer, which it had developed in conjunction with Hitachi, Ltd. The new machine, an electrophoresis -based genetic analysis system, cost US$ 300,000 each, but was a major leap beyond its predecessor, the 377, and was fully automated, allowing genetic decoding to run around the clock with little supervision. According to Venter,

2618-446: The U.S. military and other government departments. EG&G builds a variety of sensing, detection and imaging products including night vision equipment , sensors for detection of nuclear material and chemical and biological weapons agents, and a variety of acoustic sensors. The company also supplies microwave and electronic components to the government, security systems, and systems for electronic warfare and mine countermeasures. During

2695-479: The array surface and are then "spotted" onto glass. A common approach utilizes an array of fine pins or needles controlled by a robotic arm that is dipped into wells containing DNA probes and then depositing each probe at designated locations on the array surface. The resulting "grid" of probes represents the nucleic acid profiles of the prepared probes and is ready to receive complementary cDNA or cRNA "targets" derived from experimental or clinical samples. This technique

2772-430: The arrays provide intensity data for each probe or probe set indicating a relative level of hybridization with the labeled target. However, they do not truly indicate abundance levels of a gene but rather relative abundance when compared to other samples or conditions when processed in the same experiment. Each RNA molecule encounters protocol and batch-specific bias during amplification, labeling, and hybridization phases of

2849-410: The board of PE Corporation announced a two-for-one split of PE Biosystems Group Common Stock. At year end 1999, after the major divestment that year of the former Analytical Instruments Division, the new PE Corporation assets totalled over US$ 1.5 billion, split between the two Life Sciences groups. Of that, PE Biosystems Group, with 3,500 employees had net revenues of over US$ 1.2 billion. By June 2000,

2926-731: The business. The company has 5,954 employees. The new competitive genomics industry had formed for the development of new pharmaceuticals, based on the work of the Human Genome Project. The Applied Biosystems Division made thermal cyclers and automated sequencers for these new genomics companies. In 1995, Perkin-Elmer sold its 30,000th thermal cycler. To meet Human Genome Project goals, Perkin-Elmer developed mapping kits with markers every 10 million bases along each chromosome . Also that year, DNA fingerprinting using polymerase chain reaction (PCR) became accepted in court as reliable forensic evidence. In 1993, Perkin-Elmer had become

3003-550: The company was acquired by defense technical-services giant URS Corporation . URS' EG&G division is headquartered in Gaithersburg, Maryland , and employs over 11,000 people. During its heyday in the 1980s, EG&G had about 35,000 employees. In December 2009, URS announced its decision to discontinue the use of "EG&G" as a division name. The headquarters issued a press release stating that by January 1, 2010 it would discontinue using secondary corporate brands, including

3080-627: The considerations of experimental design that are discussed in the expression profiling article are of critical importance if statistically and biologically valid conclusions are to be drawn from the data. There are three main elements to consider when designing a microarray experiment. First, replication of the biological samples is essential for drawing conclusions from the experiment. Second, technical replicates (e.g. two RNA samples obtained from each experimental unit) may help to quantitate precision. The biological replicates include independent RNA extractions. Technical replicates may be two aliquots of

3157-569: The consortium announced that it had revised its timeline, and would release by the Spring of 2000 a "first draft sequence" for 80% of the human genome. On March 19, 1999, Perkin-Elmer Corporation, as a New York corporation, filed SEC Form S-4 /A, to enter a reincorporation merger with a subsidiary of PE Corporation of Delaware. Shareholders of the New York corporation stock (NYSE:PKN) would receive shares in two new stocks instead. On April 27, 1999,

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3234-650: The database business would distract from pharmaceutical development. Applied Biosystems was a better fit for the database, because Applied already had the huge sales force in place for the marketing of its instruments. Plans were to expand those sales and those of the database into an electronic commerce system. The database itself, Celera Discovery System (CDS), would remain with Celera, because of shareholder approval complications. Celera would retain responsibility for its maintenance and support to existing customers, and would receive royalties from Applied Biosystems. The database revenues were expected to reach US$ 100 million for

3311-399: The desired purpose; longer probes are more specific to individual target genes, shorter probes may be spotted in higher density across the array and are cheaper to manufacture. One technique used to produce oligonucleotide arrays include photolithographic synthesis (Affymetrix) on a silica substrate where light and light-sensitive masking agents are used to "build" a sequence one nucleotide at

3388-481: The dimensionality of the data to aid comprehension and more focused analysis. Other methods permit analysis of data consisting of a low number of biological or technical replicates ; for example, the Local Pooled Error (LPE) test pools standard deviations of genes with similar expression levels in an effort to compensate for insufficient replication. The relation between a probe and the mRNA that it

3465-604: The experiment making comparisons between genes for the same microarray uninformative. The comparison of two conditions for the same gene requires two separate single-dye hybridizations. Several popular single-channel systems are the Affymetrix "Gene Chip", Illumina "Bead Chip", Agilent single-channel arrays, the Applied Microarrays "CodeLink" arrays, and the Eppendorf "DualChip & Silverquant". One strength of

3542-539: The fourth member of their fledgling technology group. The group's high-speed photography was used to image implosion tests during the Manhattan Project . The same skills in precisely timed high-power electrical pulses also formed a key enabling technology for nuclear weapon triggers. After the war, the group continued their association with the burgeoning military nuclear effort and formally incorporated Edgerton, Germeshausen, and Grier, Inc. in 1947. During

3619-489: The future they could be used to screen seedlings at early stages to lower the number of unneeded seedlings tried out in breeding operations. Microarrays can be manufactured in different ways, depending on the number of probes under examination, costs, customization requirements, and the type of scientific question being asked. Arrays from commercial vendors may have as few as 10 probes or as many as 5 million or more micrometre-scale probes. Microarrays can be fabricated using

3696-456: The genome decoding by 2001. That bold pronouncement prompted the academic consortium to accelerate their own deadline by a couple years, to 2003. In May 1998, the company's newly formed unit to accomplish the task, Celera Genomics Group, in Rockville, Maryland, was created to become the definitive source of genomic and related medical information with the goal of sequencing the human genome by

3773-399: The genomics segment of the technology bubble was peaking. Celera Genomics (CRA) and PE Biosystems (PEB) were among five genetics pioneers leading at that time, along with Incyte Genomics ( Nasdaq :  INCY ), Human Genome Sciences ( Nasdaq :  HGSI ), and Millennium Pharmaceuticals ( Nasdaq :  MLNM ). All five of those stocks by then had exceeded a price above $ 100 a share in

3850-484: The industry. ... This change will allow us to present a single brand that is easily understood by our clients". Koffel indicated that the move to a single corporate brand would affect neither the internal organization nor the existing reporting structure. However, EG&G Division would become URS Federal Services. In 2014, URS was acquired by AECOM . In January 2020, AECOM sold its Management Services division, which provides services and support to governmental clients, to

3927-451: The level of detail that should exist and is being adopted by many journals as a requirement for the submission of papers incorporating microarray results. But MIAME does not describe the format for the information, so while many formats can support the MIAME requirements, as of 2007 no format permits verification of complete semantic compliance. The "MicroArray Quality Control (MAQC) Project"

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4004-480: The machine was so revolutionary that it could decode in a single day the same amount of genetic material that most DNA labs could produce in a year. The partnership sold hundreds of the 3700 analyzers to Celera, and also to others worldwide. The public consortium also bought one of the Applied Biosytems 3700 sequencers, and had plans to buy 200 more. The machine proved to be so fast that by late March 1999

4081-484: The market for that equipment. Hunkapiller brought in J. Craig Venter to direct the project. Tony L. White, president of the Perkin-Elmer Corporation backed Hunkapiller on the venture. Perkin-Elmer's interest was driven largely by its monopoly, through the equipment of Applied Biosystems, of the market for automated DNA sequencing machines. Venter boldly declared to the media that he would complete

4158-799: The market, before ultimately crashing back down. On November 28, 2000, PE Corporation filed SEC Form 8-K to report its announcement of the change of its name to Applera Corporation . At the same time, PE Biosystems Group changed its name to Applied Biosystems Group , and changed its ticker symbol from PEB to ABI. Both name changes became effective November 30, 2000. Also that date, the parent corporation web site address changed from https://web.archive.org/web/20070929001200/http://www.pecorporation.com/ to https://web.archive.org/web/20070822133148/http://www.applera.com:80/ The combined Applera then had 5,000 employees. PE/Applied Biosystems Group's net revenues rose to almost US$ 1.4 billion. Celera that year made milestone headlines when it announced that it had completed

4235-430: The multiple levels of replication in experimental design ( Experimental design ); the number of platforms and independent groups and data format ( Standardization ); the statistical treatment of the data ( Data analysis ); mapping each probe to the mRNA transcript that it measures ( Annotation ); the sheer volume of data and the ability to share it ( Data warehousing ). Due to the biological complexity of gene expression,

4312-528: The new PerkinElmer. At that point the remaining Connecticut Life Sciences company issued its two tracking stocks, and also changed its own name to PE Corporation . The Applied Biosystems group had earlier already been renamed PE Biosystems , and it retained that name in the first incarnation of its tracking stock. In 2000, the Applied Biosystems name was restored to the group, with the new stock ticker symbol ABI, and PE Corporation became Applera ,

4389-516: The non-government side of EG&G Inc.; formerly NYSE :  EGG ; purchased the Analytical Instruments Division of PerkinElmer for US$ 425   million (equivalent to $ 777.33   million in 2023), also assuming the PerkinElmer name ( NYSE :  PKI ). At the time EG&G was based in Wellesley, Massachusetts , and made products for diverse industries including automotive, medical, aerospace and photography. At least in 1988, there

4466-666: The only choice in some situations. Suppose i {\displaystyle i} samples need to be compared: then the number of experiments required using the two channel arrays quickly becomes unfeasible, unless a sample is used as a reference. two channel microarray (with reference) This is an example of a DNA microarray experiment which includes details for a particular case to better explain DNA microarray experiments, while listing modifications for RNA or other alternative experiments. The advent of inexpensive microarray experiments created several specific bioinformatics challenges:

4543-575: The private equity firm American Securities and Lindsay Goldberg for US$ 2.405   billion (equivalent to $ 2.83   billion in 2023); the new firm was named Amentum . EG&G's "Special Projects" division was the notable operator of the Janet Terminal at McCarran International Airport [Now Harry Reid] Las Vegas, Nevada , a service used to transport employees to remote government locations in Nevada and California. EG&G also had

4620-570: The public consortium, forecast that the project could be completed in 15 years from its 1990 starting date, at a cost of US$ 3 billion. The HGP was a public consortium of eight university centers funded through the U.S. Department of Energy , the National Institutes of Health and the Wellcome Trust of London. The government-backed project targeted completion of human DNA mapping by the year 2005. In 1993, Perkin-Elmer acquired

4697-423: The reorganization was made effective, as the Perkin-Elmer Corporation was merged into a temporarily created subsidiary of PE Corporation, a new Delaware corporation. The recapitalization of the company resulted in issuance of the two new classes of common stock, called PE Corporation-PE Biosystems Group Common Stock and PE Corporation-Celera Genomics Group Common Stock. On that date, trading began in both new stocks on

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4774-447: The same extraction. Third, spots of each cDNA clone or oligonucleotide are present as replicates (at least duplicates) on the microarray slide, to provide a measure of technical precision in each hybridization. It is critical that information about the sample preparation and handling is discussed, in order to help identify the independent units in the experiment and to avoid inflated estimates of statistical significance . Microarray data

4851-434: The same level of sensitivity compared to commercial oligonucleotide arrays, possibly owing to the small batch sizes and reduced printing efficiencies when compared to industrial manufactures of oligo arrays. In oligonucleotide microarrays , the probes are short sequences designed to match parts of the sequence of known or predicted open reading frames . Although oligonucleotide probes are often used in "spotted" microarrays,

4928-405: The samples to the array, and finally scan the arrays with their own equipment. This provides a relatively low-cost microarray that may be customized for each study, and avoids the costs of purchasing often more expensive commercial arrays that may represent vast numbers of genes that are not of interest to the investigator. Publications exist which indicate in-house spotted microarrays may not provide

5005-478: The sequencing and first assembly of the two largest genomes in history, that of the fruit fly , and of the human. In 2001, the Applied Biosystems division of Applera reached revenues of US$ 1.6 billion, and developed a new workstation instrument specifically for the new field of proteomics , which had become Celera's new core business focus, as it shifted away from gene discovery. The instrument analyzed 1,000 protein samples per hour. In January 2002, J. Craig Venter

5082-646: The shareholders of Perkin-Elmer Corporation approved the reorganization of Perkin-Elmer into a pure-play life science company, resulting in the name change to PE Corporation and the de-listing of the PKN stock. Each share of the Perkin-Elmer New York (PKN) was to be exchanged for one share and for 1 ⁄ 2 of a share respectively of the two new common share tracking stocks for the two component Life Sciences groups, PE Biosystems Group (NYSE:PEB) and Celera Genomics Group (NYSE:CRA). On April 28, 1999,

5159-512: The single-dye system lies in the fact that an aberrant sample cannot affect the raw data derived from other samples, because each array chip is exposed to only one sample (as opposed to a two-color system in which a single low-quality sample may drastically impinge on overall data precision even if the other sample was of high quality). Another benefit is that data are more easily compared to arrays from different experiments as long as batch effects have been accounted for. One channel microarray may be

5236-568: The target probes. Although absolute levels of gene expression may be determined in the two-color array in rare instances, the relative differences in expression among different spots within a sample and between samples is the preferred method of data analysis for the two-color system. Examples of providers for such microarrays includes Agilent with their Dual-Mode platform, Eppendorf with their DualChip platform for colorimetric Silverquant labeling, and TeleChem International with Arrayit . In single-channel microarrays or one-color microarrays ,

5313-534: The term "oligonucleotide array" most often refers to a specific technique of manufacturing. Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family of gene splice-variants by synthesizing this sequence directly onto the array surface instead of depositing intact sequences. Sequences may be longer (60-mer probes such as the Agilent design) or shorter (25-mer probes produced by Affymetrix ) depending on

5390-931: The two replacement tracking stocks for the new PE Corporation were issued to shareholders. The Pacific Stock Exchange began trading PE Corporation options for the two new stocks that day. Michael W. Hunkapiller remained as senior vice president of PE Corporation, and as president of PE Biosystems. Afeyan initiated and oversaw the creation of the tracking stock for Celera Genomics Group. Then later in 1999 Afeyan left, to co-found Flagship Ventures, an early-stage entrepreneurial venture capital firm. J. Craig Venter remained as senior vice president of PE Corporation and also president of Celera Genomics Group. Tony L. White remained as PE Corporation's chairman, president and chief executive officer. Other officers who remained in PE Corporation included William B. Sawch, as senior vice president, general counsel and secretary. On May 6, 1999,

5467-699: The world's leading manufacturer of instruments and reagents for (PCR). It marketed PCR reagents kits in alliance with Hoffman-La Roche Inc. In 1996, Perkin-Elmer acquired Tropix , Inc., a chemiluminescence company, for its life sciences division. Also In 1996, Tony L. White from Baxter International Inc. became president and chief executive officer of Perkin-Elmer and reorganized it into two separate operating divisions, Analytical Instruments and PE Applied Biosystems . The PE Applied Biosystems division accounted for half of Perkin-Elmer's total revenue, with net revenues up by 26%. In 1997, Perkin-Elmer revenues reached almost US$ 1.3 billion, of which PE Applied Biosystems

5544-426: The year 2001. Celera became the primary commercial competitor to the government-funded effort of the Human Genome Project. Venter became president and chief scientific officer of Celera. At the time, Venter operated his own independent lab, The Institute for Genomic Research (TIGR), which had developed a "random shotgun" approach to DNA decoding, making it the most prolific genome lab in the world. At year end 1998,

5621-551: Was US$ 653 million. Acquisitions included GenScope, Inc., and Linkage Genetics, Inc., which combined with Zoogen to form PE AgGen , focused on genetic analysis services for plant and animal breeding. Partnerships were begun with Hyseq, Inc., on the new DNA chip technology, and also with Tecan U.S., Inc., on combinatorial chemistry automation systems, and also with Molecular Informatics , Inc. on genetic data management and analysis automated systems. In 1998, Perkin-Elmer acquired PerSeptive Biosystems (formerly Nasdaq :  PBIO ),

5698-531: Was also working on the massive task. Consequently, Perkin-Elmer's people and companies became among the most famous players of the decade in biotechnology and in that segment of the technology bubble . In the process, Perkin-Elmer divided and transformed itself into Applera, a company entirely focused in life sciences. Beginning in 1990, the U.S. government approved financing to support the Human Genome Project (HGP). James D. Watson , who founded

5775-463: Was either a subsidiary or internal department of EG&G dubbed EG & G Biomolecular that produced the Acugen 402 DNA sequencer, the first (and perhaps only) commercially available automated DNA sequencer that used slab gel electrophoresis and radioactive Sanger sequencing . From 1999 until 2001, EG&G was wholly owned by The Carlyle Group . In August 2002, the defense-and-services sector of

5852-488: Was found to be more useful when compared to other similar datasets. The sheer volume of data, specialized formats (such as MIAME ), and curation efforts associated with the datasets require specialized databases to store the data. A number of open-source data warehousing solutions, such as InterMine and BioMart , have been created for the specific purpose of integrating diverse biological datasets, and also support analysis. Advances in massively parallel sequencing has led to

5929-665: Was pushed out of Celera, when it was decided that the group would make pharmaceuticals instead. Venter lacked experience in pharmaceutical development. On April 22, 2002, the Celera Genomics Group announced its decision to abandon what had been its core business since its 1998 inception, and to shift the role of marketing data from its genetic database over to its sister company, the Applied Biosystems Group. Celera would instead develop pharmaceutical drugs. Applera CEO Tony L. White had noted earlier that

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