DNA microarray

Microarray technique
. you are here->home->Biotechnology and Biomedical Engineering->Systems Biology Virtual Lab->Integrating Biological Networks and Microarray Expression data. ... Gene expression can observed by different experimental techniques such as Northern blot, serial analysis of gene expression (SAGE), Western blot, DNA microarray, RNA-Seq etc.
6 April
SCIENCE CONCEPTS: Genetic correlation to disease, DNA gene sequencing, pharmacogenetics, personalized medicine, gene expression, diagnosing disease and microarray lab applications. OVERALL TIME ESTIMATE: The unit will take six school periods of 50 minutes each. ... Pharmacogenomics Curriculum – Ms. Escoto. Page 6. VOCABULARY: The vocabulary of the unit will be all related to DNA, Protein Synthesis, Cell Structure, Laboratory Techniques, Genetics and Pharmacogenetics.
DNA Microarrays (Gene Chips)
• Gensphere Teacher Resources: A laboratory kit (DNA Chips: Genes to Disease, A Hands-on Wet Lab) that costs approximately $70. ... Life Sciences Learning Center – Cancer Education Project Copyright © 2007, University of Rochester May be copied for classroom use. 3. Microarrays and Cancer. • Profiling Technique: Microarray Analysis: An online tutorial on pharmacogenomics and personalized medicine.
This Virtual Lab is broken up into three chapters. Chapters 1 and 2 will give you some background and review a couple of important concepts that will help you understand DNA Microarray technology. Chapter 3 is the experiment. Chapter 2 Measuring Gene Expression. ... Press NEXT to continue. Scientists rely on a technique called protein expression analysis to tell them if the mRNA is being translated into protein.
DNA Microarrays Virtual Lab
DNA Microarrays Virtual Laboratory Exercise. Name: Instructions: 1. Visit the following website: 2. Click on the Microarray to begin. ... 22. What technique do scientists use to study whether the mRNA is actually being translated? 23. Summarize the major limitations of DNA microarray analysis.
International Journal for Pharmaceutical Research Scholars (IJPRS) ISSN No: 2277-7873 REVIEW ARTICLE V-1, I-4, 2012 DNA Microarray Technique Thakare SP*, Trivedi PK, Jani PH, Patel GV Department of Pharmacology, Sigma Institute of Pharmacy, At – Bakrol, Dist – Vadodara, Gujarat, India Manuscript No: IJPRS/V1/I4/00196, Received On: 26/10/2012, Accepted On: 06/11/2012 ABSTRACT DNA Microarray.
22 April
DNA Microarrays
§ DNA probes are synthesized and then “spotted” onto the microarray. § Customized for each experiment “in-lab”. § Low cost. Oligonucleotide microarrays. § DNA oligonucleotides are synthezised directly on the microarray. § Commercial arrays (Affymetrix, Nimblegen and Combimatrix). § expensive.
DNA Microarrays
The DNA microarray is one of the more recent advances in toxicogenomics. Microarrays have the ability to detect “changes in gene expression associated with specific types of toxic response.” (7) A DNA chip contains sequences of known genes that have been attached when manufactured. In the lab two samples are prepared, one being exposed to the putative toxicant. RNA is then isolated and extracted. Reverse transcriptase is used to create cDNA which is single stranded.
26 December
Analyzing DNA Microarrays
DNA microarrays are able to simultaneously measure thousands of genes (and the activity of those genes) in a single sample. Biologists use microarrays to trace connections between pathways or to identify all genes that respond to a signal. ... The project materials include readings on microarrays as well as computer lab activities. The topics covered include image analysis, filtering and normalization techniques, and statistical methods.
Quantitative Genomics & Microarray Core Lab - UTHealth
The facility can perform all techniques associated with a qPCR instrument, quantitative Meso Scale ELISAs, and microarrays utilizing Illumina and Agilent arrays. ... The Nanochemistry Service Center provides custom synthesis, labeling, and chemical coupling of DNA thioaptamers and nanoparticles. The Director and Lab Manager are both PhD chemists with years of experience in DNA synthesis, especially the more difficult monothioated and dithioated DNA.
6 February
DNA microarrays for malaria
Specifically, DNA microarrays can simultaneously analyze expression of thousands of malaria genes in a single experiment [6–8]. Such techniques are powerful in general, particularly for malaria research, because of the limitations of molecular genetics in malaria systems [6]. ... Microarray-based expression analysis DNA microarrays (constructed from pre-synthesized DNA) and DNA chips (involving in situ DNA synthesis using light-directed chemistry) contain high density microscopic arrangements of immobilized nucleic acids.
Chapter 8 A. Recombinant DNA Technology
Techniques of Recombinant DNA How do we manipulate these natural processes for biotechnology; for instance, to make a bacterium that produces large quantities of insulin? ... PCR Experiment in Microbiology Lab ... DNA Microarrays.
26 November
McClelland Lab
Michael McClelland’s lab works in the area of genomics, a field that aims to interpret the language of DNA. Salmonella genomics: Dr McClelland organizes the sequencing of major pathogens, including Salmonella enterica sv Typhimurium, resulting in papers in Nature and Nature Genetics. The lab provides microarray resources and techniques to over 50 labs worldwide for study of Salmonella genomes, transcription, and mutant library screens.
9 November
Bas de Heij, Roland Zengerle and Martina Daub
www.rsc.org/loc | Lab on a Chip. Fast and reliable protein microarray production by a new drop-in-drop technique. ... In contrast to DNA microarrays, production of protein microarrays is an immense technological challenge due to high complexity and diversity of proteins. In this paper we investigate three essential aspects of protein microarray fabrication based on the highly parallel and non-contact TopSpot1 technology: evaporation of probes during long lasting production times, optimization of protein immobilization and improvement of protein microarray reproducibility.
7. methods for rna and dna microarrays
laboratory techniques, such as quantitative PCR, flow cytometry or immunohistochemistry, are remarkable examples that place basic science closer to clinical medicine.8 A different DNA microarray technology, termed comparative genomic hybridization (CGH) to ... STEP 1. Genomic DNA Preparation. To minimize contamination of the simples, the use of two separate rooms to perform the assay is recomended: one is the pre-PCR clean room (or area for the DNA template and free of PCR products), and the other is the PCR-Staging room or main lab, where the rest of steps are performed.
DNA Microarray Technology Workshop: A Comprehensive...
Course Description This comprehensive, hands-on workshop on DNA microarrays is designed for investigators contemplating or pursuing studies in differential gene expression. This entry-level workshop will lead participants through the processes and techniques for designing, printing, hybridizing, scanning, and analyzing microarrays. Daily Schedule Monday • Morning. Lecture (348B NRC): Introduction to the workshop and DNA microarray technology Laboratory (144 NRC): Preparation of tagged cDNA target Part I, cDNA synthesis • Afternoon Laboratory (144 NRC)...
Course Description
Provides students with advanced laboratory skills needed for employment in the biotechnology industry. Focuses on use of basic and specialized lab equipment and techniques such as solution chemistry, cell culture, DNA extraction and analysis, protein extraction and analysis. ... A significant portion of time will also be spent covering newer DNA technologies including the polymerase chain reaction (including real-time PCR), DNA sequencing, DNA fingerprinting (using AFLP and microsatellite techniques) and microarrays.
Lab 2 - Analysis of Affymetrix Microarray Data
For this lab, we will use data from a set of eight Affymetrix chips from a 2x2 factorial-design experiment designed to measure changes in gene expression in a breast-cancer cell line due to the presence (or absence) of estrogen and due to a time effect (10 hours or 48 hours). ... Thanks also to Robert Gentleman and Wolfgang Huber for the vignette in the estrogen package which this lab was based on. Thanks also to Sandrine Dudoit, Robert Gentleman, Rafael Irizarry, and Yee Hwa Yang for the DNA Microarray Data and Oligonucleotide Arrays talk slides from the Bioconductor Short Course at DSC 2003 in...
8 October
DNA Microarray (Genome Chip) (by Leming Shi, PhD)
DNA Microarray Technology to identify genes controlling spermatogenesis, Sam Ward at the University of Arizona. Vivian Cheung's Lab at The Children's Hospital of Philadelphia focuses on the development of Direct Identical-by-Descent (IBD) Mapping, which is a DNA microarray-based mapping technique that allows isolation and mapping of DNA fragments shared IBD between individuals. University of Washington, Dr. Lee Hood, Java-based Array Image Spot Finding and Quantification Software (CrazyQuant).
9 October
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18 March
Chapter 5: Microarray Techniques
?Created microarray with 18k probes. — 1/4 of the genes were replicated to assure reproducibility — 128 array experiments using 96 test samples and 1 control sample — log(T/C) measures relative level of fluorescence of test/control. ?Clustered co-expressed genes based on expression profile. ... consuming. • Short sequences are not as specic for. target DNA. Limitations • Isolation of individual cDNAs to immobilize.
Microarrays and Data Analysis
DNA Microarrays in the Undergraduate Microbiology Lab: Experimentation and Handling Large Datasets in as Few as Six Weeks. David B. Kushner* Department of Biology, Dickinson College, Carlisle, Pennsylvania 17013. DNA microarrays have significantly impacted the study of gene expression on a genome-wide level but also have forced a ... In response to these teaching techniques, students should begin to develop higher-order cognitive skills, such as conceptual reasoning, that are required for progression through the undergraduate curriculum (2, 16, 23). Active-learning techniques such as problem-based
Comparing whole genomes using DNA microarrays
DNA microarrays present an alternative way to study differences between closely related genomes. Advances in microarray-based approaches have enabled the main forms of genomic variation (amplifications, deletions, insertions, rearrangements and base-pair changes) to be detected using techniques that are readily performed in individual laboratories using simple experimental approaches.
Drosophila RNAi Microarray Home Page
Acknowledgements. Sabatini Lab Website. The Whitehead Institute for Biomedical ... This website describes a technique for rapid microarray-based analysis of RNA interference ... Add 5 ul of each template DNA to a 20 ul (final volume) in-vitro transcription reaction as...
28 January
Signal Processing Techniques in Genomic
The fabrication of the DNA microarray can be done with the spotting method [36] or on-chip synthesis [37], [38]. The target genes are normally required to be amplified and labeled with fluorescence. Multicolored fluorescent techniques are often used in comparative hybridization detection. ... His Neural Engineering and Informatics Lab is interested in investigating the motor functions of patients with Parkinson’s disease and the effect of developmental abnormalities and maturation on the dynamics of respiration.
DNA Microarrays
However readers could benefit from learning something about the technical basis of DNA microarrays, and younger readers may be curious to know some-thing of the origins and antecedents of this new technology. In this chapter, I have attempted also a critical overview of the current state of the art. ... The method used to fix chromosomes and nuclei to microscope slides in a way that allowed the DNA to take part in duplex formation with the probe is now used to fix DNA spotted on to slides in one microarray method. And the multicolor fluorescent labeling techniques introduced by Ried et al.
DNA Microarrays
Data Access Experimental Conditions and RNA Isolation Affymetrix GeneChip® Arrays Spotted DNA Microarrays. ... E. coli microarrays provided by the Gene Expression Center on the UW Campus were used in our lab. These microarrays contain more than 95% of the 4,290 ORFs initially identified in the E. coli K-12 genome, as well as a variety of positive and negative controls. PCR products are double spotted onto poly-lysine coated microscope slides using standard methods.
29 October
Label-Free Prehybridization DNA Microarray
Technical variability during DNA capture probe printing remains an important obstacle to obtaining high quality data from microarray experiments. While methods that use uorescent labels for visualizing printed arrays prior to hybridization have been presented, the ability to measure spot density using label-free techniques would provide valuable ... DNA microarrays are an important tool for the highly parallel study of expression levels of multiple genes of interest. However, microarray data has been shown to lack reproducibility,1 which in part is due to variability in array printing.2 Custom arrays that.
I. The traditional techniques of RNA analysis
Complementary DNA (cDNA): An enzyme called reverse transcriptase can copy RNA molecules into DNA. Because its sequence is the reverse complement of the RNA sequence it is called complementary DNA. This is a very useful technique in the lab, and cDNA is commonly used to make probes that represent an RNA sample. 1. Genomics and Computational Biology Section 4: Microarrays and Sequencing. Oct.
Novel Patterning Techniques for DNA-sensing Microarray...
This microarray is associated with a large background fluorescence signal. Another commercially available microarray utilizes a pin-robot, which deposits a mixture of probe DNA and polyacrylamide gel onto the glass slide. This produces round pads in the array that already have the gel and probe DNA incorporated. ... APL scientists have developed novel techniques to create patterned DNA microarrays. These techniques minimize background fluorescence, reduce false positives, and allow for uniform spot size.
3 January
DNA Microarray Lab in a Molecular Biology Course
More recent activities are detailed above. DNA Microarray Lab in a Molecular Biology Course. Stephan Zweifel. ... In addition to introducing students to a current genomics technique, this is an example of what one can accomplish with the wealth of DNA sequence information currently available. The hope is that students who have this laboratory experience will shed preconceived notions about the compartmentalization of the cell, and start viewing the cell as an interconnected network of gene regulatory pathways.
11 May
Biology 390, Molecular Techniques, Fall 2015
Laboratory exercises include DNA, RNA, and protein manipulations, web-based sequence analysis, and the use of associated apparatus. Lectures cover background information of the techniques and their applications. ... Week 8: 10/20/2015. Quiz: Yes Lecture: DNA Microarray Analysis Laboratory: Microarray Analysis II: Data Analysis Required reading: Miller and Tang, pages 1-11.
Chapter 13 | Two daughter DNA molecules
Making DNA molecules. • In your cells (DNA replication)! • In the lab! – Probes! – Primers! – Products of PCR! • Techniques related to making DNA molecules/uses of synthetic DNA molecules! – Southern blotting, Northern blotting! – Microarrays! ... • We have learned about nucleic acid probes and several applications of probes in biotech! • Now, we will learn about primers, what they are, why they are needed both in cells and in the lab! – To start off, let’s go back to review DNA replication! Polymerase Chain Reaction (PCR).
Microarray challenges in ecology
Oligo microarray: a microarray that uses probes comprising synthesized pieces of DNA of uniform length ($ 40–80 base pairs). This can lead to more comparable signals than acquired using cDNA microarrays, but the technique is usually only used for organisms with completely sequenced genomes. qRT-PCR: a technique that is used in combination with reverse-transcription PCR to quantify small amounts of mRNA in a sample. ... Lab Lab Lab Lab Semi-eld.
2011 Lab 8 - CellBiology
2011 Lab 8. From CellBiology. Jump to:navigation, search. Contents. 1 Microarray Laboratory. 1.1 Introduction. ... You are invited to attend a seminar which will highlight Basic Components of Cell Culture, Aseptic Techniques, Aspiration Techniques, and Techniques for Culturing. Product Specialists will be available to answer your questions and discuss your applications. Date: Friday 13th May 11.00 am – 11.45 am.
5 August
Microarray studies and other genomic techniques are also stimulating the discovery of new targets for the treatment of diseases which may help for drug development. Since characteristic patterns of gene expression can be measured in parallel by using microarrays, gene expression profiling with DNA microarrays has emerged as a powerful approach to study the abundance of RNA for targeted genes of biological samples. The Microarray Facility provides instrumentation and expertise for analysis of gene expression using Affymetrix GeneChip microarrays. The Microarray Facility lab is located in the...
21 December
Microarray applications and challenges: a vast array of...
Microarray systems: The basic types of DNA microarrays include sequencing chips ... Pevsner Lab’s (Kennedy Krieger Institute) Young lab (White head institute-MIT) Another Microarray Database. ... There are many microarray techniques with clinical applications.
Biology 437
1. Biology 437: LABORATORY ON DNA MANIPULATION Syllabus 2012 ... Computer-based analysis using microarrays to provide sampling of what data is generated. ... techniques, ESTs. NOV 2: LAB 9A: Set up PCR product and vector for cloning; clean and.
Microarray - How Does It Work? | Unsolved Mysteries of...
Microarray. Something’s Fishy. Getting Started. ... Measuring Gene Expression. In the Lab. How Does It Work? Data Analysis.
27 September
Curriculum vitae | technical skills
1999 to 2000 Certificate of Medical Laboratory Technician Course, Dept. of Bio-Medical Lab. Technology, Vivekanandha Institute of Medical Science and Research, Thiruchenkodu, Tamilnadu, India (Medical Educations, Govt. of Tamilnadu, India) Laboratory Techniques : Pathology, biochemistry and Microbiology. ... – Pande-Rath “First Prize winner”. · August, 2007 – Centre for Marine Science and Technology, MS University, Tamilnadu, India – EMBO World Practical Course on “DNA Microarray: Analysis and applications”. · December 2005 Centre for Potential Genomic Sciences...
BMC Genomics | Table 1: Construction of DNA microarray
We describe the successful construction and use of DNA microarrays by the two-stage amplification approach and discuss the technical challenges that were met and resolved during the project. ... We also describe the techniques utilized to optimize hybridization conditions and signal-to-noise ratio of the transcription profile. The inter-lab transportability was demonstrated by the virtual error-free amplification of the entire genome complement of 3,168 genes using the universal primers in partner labs.
Array Based Cancer Diagnostics Gene Expression Profiling of...
DNA microarray technology is a powerful mean for exploring genome of organisms. It is an important tool for monitoring and analyzing gene expression profiles of thousands of genes simultaneously. Their small size, high densities and compatibility with fluorescent labeling make microarray technology a widely used technique in the area of molecular genetics. ... Count Tree Technology Lab Notes, Technical Report NDSU-CSOR-TR-01-1.
Microarray Data from a | Advanced Techniques
There are several techniques for constructing DNA microarrays (Schena et al. ... two samples have similar activity, and the black spots indicate where there is no activity. An example of some microarray data is given in Table 1. The data came from an experiment on aging yeast in Laura Hoopes’ lab at Pomona College. The test sample (treatment) contains older yeast cells, while the reference sample (control) contains younger yeast cells.
Microarray Hybridization | Labeling DNA
2003). The sample DNA, or more usually PCR product derived from it, is labeled with a fluorophore so that the specific sites of hybridization on the microarray can be visualized and the intensity of the hybridization signal quantified. The method is conceptually identical to Southern hybridization of a dot blot, but ... This allows quantitative differentiation between transcription levels in the two samples when the relative difference in abundance is greater than about two-fold (Quackenbush 2002). Using the same technique, it should be possible to quantitate >2-fold differences in species abundance between two ecological samples.
16 February
Genome Consortium for Active Teaching - GCAT
The BIO 580 students will be expected to work independently on labs and put together a presentation comparing the microarray technique with the technique of using RT-PCR. What are the advantages and disadvantages of each technique? ... Inoculate clone cultures (the day before lab) Preparation of plasmid DNA from clones. Culture Preparation Plasmid Miniprep Exploring Databases.
13 January
DNA Microarrays: Theory, Techniques and Analysis
Fax: Please include area code. Register by Mail Mail completed form and payment to: Conference & Event Services Attn: DNA Microarrays University of California, Davis One Shields Avenue 442 Memorial Union Davis, CA 95616. UC Affiliate: Grad Student_____ Post Doc_____ Faculty _____ Tech Staff _____ Non UC _____. ... Lecture and Lab are limited to 25 participants. Course will be filled on a first-come, first-served basis. UCD – DEB Grad Students.
Microarray data analysis tool using java
Chapter two discusses microarray analysis techniques, including an overview of log ratios, normalization, visualization plots, differentially expressed genes using the fold change method, and clustering. Chapter three is a literature review of existing microarray data analysis software, their drawbacks and how the system being developed caters to the needs of the user who ... 1.8 Microarrays Microarrays, developed in the lab of professor Patrick Brown at Stanford, in the. early 1990’s, took molecular biology by storm[7]. They are small slides spotted with fixed samples of DNA, each for a different gene.
UC Berkeley | Functional Genomics Laboratory | Research...
Complementing the high-throughput DNA sequencing capabilities of the Vincent J. Coates Genomic Sequencing Laboratory, the FGL specializes in the fabrication, use, and analysis of DNA microarrays for large-scale gene expression profiling and genetic profiling, and provides full core lab services for Affymetrix GeneChip arrays and Agilent DNA microarrays. FGL scientists are actively involved in the development of new techniques for microarray-based experimentation and statistical approaches for analyzing complex datasets.
19 April
Subject Area(s)
New techniques such as the DNA microarray allow for the rapid sequencing of genes and are based on recent advancements in nanotechnology fabrication. This lesson introduces students to the concept of rapid DNA sequencing using the DNA microarray and DNA hybridization. ... Genetics Lab. Engineering Connection. Chemical engineers and biologists use genetic manipulation to study the role of genetic diseases and the predisposition of certain individuals to certain disease.
DNA Arrays
Some areas in which microarrays play a major role: • gene regulation • development • evolution • disease. One common use of DNA arrays is to determine which genes are activated and which genes are repressed when two populations of cells are compared. All genes are measured simultaneously. ... Most successful experiments consist of both biological and technical replicates. -----Sources: 1) Exploration and Analysis of DNA Microarray and Protein Array Data by Dhammika Amaratunga and Javier Cabrera.
Compressed Sensing DNA Microarrays
To overcome these limitations, it has been proposed that a DNA microarray based on the theory of Compressed Sensing (CS) - a Compressed Sensing Microarray - would require fewer “intelligently chosen” sensors to identify the same number of organisms [2]. Compressed sensing is an emerging signal-processing technique that applies to signals with sparse, or at least rapidly decaying, representation in some orthogonal basis. [3–5]. As with other com-pression techniques, it extracts the minimal information required to accurately reconstruct the signal.
BIO SCI 1983 Introduction to Biomedical Problems (LEC 3.0)
4. Organ failure a. Protein biosynthesis i. Ribosomes, protein purification, electrophoresis. b. Organ transplant; organ donors; tissue matching c. Tissue engineering. Laboratory Techniques ELISA DNA microarray Biofeedback (EEG) Serial dilutions Models: ear; plasmid; arm; protein DAN amplification DNA extraction, PCR, restriction analysis Histology of cancer and normal cells Effectiveness of UV blockers SNP profile analysis Plasmid transfection Column chromatography (protein purification) Blood matching.
Microarray Overview | Types of DNA microarrays
DNA microarray technology (also known as DNA arrays, DNA chips or biochips) represents one of the latest breakthroughs and indeed major achievements in experimental molecular biology. This novel technology, which started to appear during the second half of the 1990s, has historically evolved from the initial experimental reports published in the mid 1970s which indicated that labelled nucleic acids could be used to monitor the expression of nucleic acid molecules attached to a solid support.
Nucleic acid detection techniques for adventitious
To determine whether microarray and NGS can reliably detect multiple viruses in a sample, a novel DNA microarray and Illumina sequencing were used to detect a panel of mammalian and avian viruses. All viruses were tested both individually and in combinations. ... The analysis of microarray and NGS data requires a much larger reliance on computational resources than typical laboratory techniques.
DNA Microarrays I. Visit to Microarray Lab. 8-Feb. ... Most meetings take place on Tuesdays in the Economics building, Room 200. Special dates and venues are in italics. The Microarray Laboratory is in the Marley Building, Room 822.
18 February
Clinical laboratory instrumentation | DNA Microarray
DNA Microarray. n Applications: q Identification of complex genetic diseases q Cancer diagnosis q Drug discovery. ... 35. Standard histological technique. n Fixation n Processing. q Dehydration q Clearing q Infiltration q Embedding. n Sectioning n Staining (H&E: haematoxylin & eosin). 36. Standard histological technique. n Fixation. q Chemical: formaldehyde q Aims: n Close to a living form n Prevent alteration from subsequent treatment.
My Webspace files
24 June
Assessment of Data Processing to Improve
DNA microarray technology has been quickly adapted by mainstream laboratories to explore gene expression pro-files of part or whole-genome for an organism [1,2]. A number of microarray studies use an experimental design in which experimental and reference RNA samples are transcribed into cDNA molecules, labeled with different fluorescent dyes ... However, the reliability of the comparison is often questionable since microarray is notorious for its consid-erable fluctuation of signals. In this report, we test a vari-ety of data processing techniques in order to improve data quality in type 2 experiments.
Self-Contained, Fully Integrated Biochip for Sample
Robin Hui Liu,*,† Jianing Yang,† Ralf Lenigk,† Justin Bonanno,† and Piotr Grodzinski*,‡ Microfluidics Laboratory, Motorola Labs, Tempe, Arizona 85284. ... Anderson et al. reported an integrated system that performed RNA purification from a serum lysate, followed by PCR, serial enzymatic reactions, and nucleic acid hybridization.3 Yuen et al. reported a microchip module design for blood sample preparation (white blood cell isolation), PCR, and DNA microarray analysis.8 Lack of efficient, yet simple in design, on-chip mixing, valving, and pumping techniques and.
Biology 382 – Techniques in Molecular Biology – Syllabus...
Lab: DNA Restriction and Electrophoresis Lab report due Tues., Feb. 26. Hourly Exam / Practical Exam (basic techniques to date) Break Discuss revisions of URC abstract. Lecture: Nucleic acid purification, quantification Lab: Purification and Characterization of Plasmid DNA (Evening before: set ... Lab: Project 1 begins: Retrieve genomic sequences, design PCR primers (using ‘Primer 3’), order primers (as needed). Lecture: Genomics (whole genome sequencing), Gibson cloning, functional genomics (microarrays, KO mutants, RNA interference). Lab: Project 1 - Purify genomic DNAs for PCR, plan PCRs.
QB 826, Introduction to Quantitative Biology Techniques
The main focus of this course is not so much to learn numerous techniques, but for students coming from different backgrounds ... Bio lab: Genomic DNA purification, PCR, agarose gel electrophoresis (Vieille). ... PM: Computer lab: Microarray data analysis (Cui).
Attachment 2. Comparison of Microarray Data from Multiple...
« Previous: Attachment 1. Experimental Objectives of DNA Microarray Studies. ... In the cases where the same lab created all the microarray data it was clear that they had more experience with one of the platforms being compared. The lab effect has been shown to be particularly strong. For example, in a 1972 paper, W.J. Youden (Youden 1972) pointed out how different Physics labs published speeds of light estimates with confidence intervals that made the differences between labs statistically significant (see Figure 2-1).
9 October
DNA Microarray Experiments: Biological and Technological...
SUMMARY.DNA microarray technologies, such as cDNA and oligonucleotide microarrays, promise to rev-olutionize biological research and further our understanding of biological processes. Due t o the complex nature and sheer amount of data produced from microarray experiments, biologists have sought the collab-oration of experts ... Cependant, la complexit6 biologique et technique des expbriences de microarrays n’est pas facilement accessible aux experts analytiques. Un objectif de cette revue est de presenter les aspects biologiques et techniques essentiels B la comprkhension de telles ktudes.
DNA Microarrays: The Technical Foundations
DNA Microarrays are small, solid supports onto which the sequences from thousands of different genes are immobilized, or attached, at fixed locations. The supports themselves are usually glass microscope slides, the size of two side-by-side pinky fingers, but can also be silicon chips or nylon membranes. ... One might ask, how does a scientist extract information about a disease condition from a dime-sized glass or silicon chip containing thousands of individual gene sequences? The whole process is based on hybridization probing, a technique that uses fluorescently labeled nucleic acid molecules as "mobile...
University of Nebraska DNA Microarray Core Facility
The Microarray Core Facility functions as a full service facility for academic researchers statewide. Redirect.
20 February
Reliability and reproducibility issues in DNA microarray...
Although all DNA microarrays are based on hybridization of nucleic acid strands, the available technical choices differ widely between platforms [2]. An important distinction is the length of the probes. ... Each of these approaches has its own requirements in terms of the amount of RNA needed, data acquisition, and transformation and normal-ization techniques [3]. These requirements together with the differences in types and composition of probes, deposition technologies, and labeling and hybridization protocols, frequently result in poor reproducibility of results from one platform to another.
DNA microarray technologies for
DNA microarray technologies for measuring protein–DNA interactions Martha L Bulyk. DNA-binding proteins have key roles in many cellular processes, including transcriptional regulation and replication. Microarray-based technologies permit the high-throughput identication of binding sites and enable the functional roles of these binding proteins to be elucidated. ... Also of signicant interest is the location of histones and their post-translational modications, as they too contribute signicantly to gene regulation. The labor involved in traditional techniques.
DNA Microarray Core: Core Facilities – UT Southwestern...
15 December
Untitled Document
Identification and Removal of Contaminating Fluorescence from Commercial and In-house Printed DNA Microarrays M. Juanita Martinez1, Anthony D. Aragon1, Angelina L. Rodriguez1, Jose M. Weber1, Jerilyn A. Timlin2, Michael B. Sinclair2, David M. Haaland2, and Margaret Werner- Washburne1, 3 1 Department of Biology, University of New Mexico, Albuquerque ... Current software and normalization techniques for microarray analysis rely on the assumption that fluorescent background within spots is essentially the same throughout the glass slide and can be measured by fluorescence surrounding the spots.
25 April
DNA Microarray for CGH & Gene Expression Analyzer
Laser-saver feature enables programmability to turn on and off according to a given lab>s ?workflow needs, thereby increasing the laser’s lifespan while reducing instrument maintenance. Automate extraction and analysis of Agilent microarrays with hands-free grid placement and a ?barcode-enabled data tracking linked to microarray design and analysis protocols. ... Agilent’s Chip DNA assays allow you to automatically size and quantitate PCR fragments and restriction digests accurately and reproducibly. PCR and RT-PCR are among the most widely used techniques in molecular biology. While in some cases, it is...
21 August
Lecture 08: Miniaturization in the Life Sciences 2
nanobioSensors & MicroActuators Learning Lab. [The Genetic Code] DNA. DNA (deoxyribonuclecid acid). ... SMALL for Big Things. nanobioSensors & MicroActuators Learning Lab. [Microarray] DNA Hybridization. Strategy is in selective attachment of molecules for screening. ? Use robot to spot many “target” molecules (DNA or protein).
Swiffy output
Links to the page contain: html5 version of animation for iPad showing a viral DNA genome......
1 January
This week in bioinformatics. U DNA Microarrays. A Measuring gene expressions A Creating a microarray A Single dye vs. two-dye microarray. U Analysis of microarray data. ... U Perhaps the most commonly used technique for microarray data analysis is (hierarchical) cluster analysis. A Used in identification of common patterns of gene expression: which genes are co-expressed, which ones are over-expressed and which ones are under-expressed compared to others.
Cleveland State University
Thank you for the good company and excellent advice and help in the lab. ... DNA methylation research can be approached from a wide range of techniques. ... 2.1 Introduction. DNA microarrays are miniature arrays of DNA fragments attached to solid...
Microarray Scanner to | Immobilized DNA Verification
With the introduction of the first commercial microarray scanner, originally by GSI Lumonics, the ScanArray line offered the only upgradeable 2-wavelength scanner, the only scanning instrument to have patents that covered acquisition, barcoding and automation, and today is the brand most often found in microarray labs worldwide. ... For more information on these Array Quality Control methods, request Technical Note 600. ScanArray Express fluorescence image of EtBr stained cDNA microarray. DNA was spotted in 8 dilutions as shown. 3.
Dolan DNA Learning Center - Extraction
Filters: Catalog: All catalogs Eugenics Archive DNA Interactive Genes to Cognition Inside Cancer.
27 October
Microarrays: Theo By Rich Jenkins MS Student Genetics Prior techniques were sufficient for limited studies But completion of genomic studies open Enter Mi Types o Oligonucleotide arrays - Commonly called DNA chips - Affymetrix and others - 5-50 mer oligos per probe - multiple p Types o cDNA arrays - Commonly called DNA microarrays - 500-5000nt per probe - 1 probe per gene - <1 Attachment cDNA Synth.
Today’s | DNA Microarray Uses
n We refer specifically to DNA microarrays n DNA: deoxyribonucleic acid n microarray: n micro-. n tiny; 1/1,000,000; ? (Greek mu). n (Prefix is from Greek mikros, meaning small.) n array – grid; lots of things spread out. n So is a microarray a tiny array, or an array of tiny things? DNA Microarray Structure. ... n Chip results can be archived. n ...and reused by many labs when needed.
Course Syllabus: Post-Genomic Analysis (BIOL 5354)
5th week (2/15/2006) Dr. Byers: Microarry Analysis of Gene Expression (lab). 6th week (2/22/2006) Dr. Zhang: Applied Research with DNA Microarrays. Lab: DNA sequencing and sequence analysis. ... purification, SDS-PAGE gel, gel transfer, Western blot, etc. 4. DNA microarray: lab demonstration 5. Proteomics: lab demonstration. Syllabus STAT 5354 Post-Genomic Analysis: Statistics Part. Multivariate Data Analysis Spring 2006.
Using Gene Chips to Study the Genetics of Lung
1. gene chips (DNA microarrays) are a powerful new technology that scientists use to measure the activity (transcription) of thousands of genes at one time; 2. microarrays highlight important connections between genetics, cell biology, genes, DNA, chromosomes, gene expressions, transcription, cancer biology, proteins ... It is important to have a discussion with students prior to the lab that cancerous effects can be caused by both over- and under-expression of certain genes, and that some genes on being tested may fall into either “housekeeping” or specific to cell type, in which case they would express differently.
Dna-microarray analysis of
Therefore, reproducibility between laboratories and DNA-microarray platforms is an important issue. The key to addressing this problem is the public availability of raw data. Groups that identify clinically relevant gene-expression signatures need to be able to validate them on independent data sets from other institutions. ... 65. Sallinen, S. L. et al. Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. Cancer Res.
Microarrays Lecture Notes (no wet lab)
Centre of Excellence in Molecualr Biology
2nd international training workshop on dna microarray for gene ... This technique in combination with knowledge in bioinformatics can yield ample amount ... The course is divided into two parts: Part I will cover wet-lab aspects of microarray e.g...
26 December
DNA Microarray Virtual Lab — HCC Learning Web
Online Science GAMES, Interactive TUTORIALS, and VIRTUAL LABS.
5 August
Imaging and Image Analysis of Tissue | DNA Microarray
l High throughput techniques such as DNA microarrays, serial analysis of gene expression (SAGE) and proteomic surveys have produced many new potential diagnostic, prognostic and therapeutic targets that may lead to clinically useful applications. Tissue microarray technology for high-throughput molecular profiling of tumor specimens Kononen J et.al. ... Dako/Zeiss: ACIS II. Olympus/Bacus Labs: BLISS. 2 2 2.37. Megabytes, Gigabytes & Terabytes.
Pat Brown’s Lab Department of Biochemistry, Stanford...
brown lab microenvironment microenvironment gene expression open access open access NA microarray genomics RNA binding protein translation microarray genomics DNA microarray genomics RNA binding protein translation microarray genomics DNA microarray genomics RNA binding protein translation microarray genomics DNA microarray genomics RNA binding protein translation microarray genomics DNA microarray genomics RNA binding protein tumor stroma translation microarray genomics DNA microarray genomics RNA binding protein.
16 December
DNA Analysis: DNA microarray example: As a scientist, you are interested in the differences in expression patterns between normal human cells and cancer cells A DNA microarray can be constructed that has enough space for 40,000 – 60,000 known genes Remember that it is estimated that the human genome only has 30,000+ genes There are several ways to construct your microarray. Deposit known exons onto the chip chemically Photolithography An empty g Attach nucleotides and an The protector group is photoliable.
Untitled Document
DNA Microarray Links. Telechem Microarray E Library. ... Microarray Data Analysis Papers.
24 September
Project MLeXAI: Projects - Using a Support Vector Machine to...
A DNA microarray is a small silicon chip that is covered with thousands of spots of DNA of known sequence. Biologists use microarrays to study gene expression patterns in a wide range of medical and scientific applications. For example, analysis of microarrays has led to discovery of genomic patterns that distinguish cancerous from non-cancerous cells. ... A support vector machine (SVM) is a powerful machine learning technique that is used in a variety of data mining applications, including the analysis of DNA microarrays.
21 May
CSRC :: Colloquium Display
Computational Science Research Center :: 5500 Campanile Drive :: San Diego, CA 92182-1245 :: (619) 594-3430 ?2011 Computational Science Research Center, SDSU - All rights reserved.
31 December
DNA Microarray Data Analysis and Mining
The DNA microarray, also known as genome chip, biochip, DNA chip, gene array and GeneChip® (a registered trademark owned by Affymetrix, Inc, CA) is an approach provided to accomplish this quest. DNA microarray is currently one of the fastest developing tools in the biological sciences. ... Since the microarray technology was developed independently from multiple sources, different microarray techniques are available in the market vis-a-vis the number, type, sequence of probes, solid supports, sample preparations, and labeling systems.
MLAB 2378 Fundamentals of Molecular Diagnostics Schedule
MLAB 2337 Molecular Diagnostics Techniques. ... Lab 5. DNA Isolation Lab 6. Polymerase Chain Reaction Lab 7. Electrophoresis Lab 8. Biorad PV92 Upload completed Study Questions into Assignments ... Review the Virochip DNA Microarray presentation.
2 December
Overview of the DNA Microarray Service
Overview of the DNA Microarray Service. We have developed comprehensive facility for cDNA and oligonucleotide microarray based studies. Particular attention has been paid to provide the investigator with a report of their submitted samples that is statistically validated and richly annotated. The core is committed to be of benefit to a broad range of users and is capable of performing highly customized services.
10 December
Renn Lab thesis reserach Quinn Langdon
Renn Lab Thesis Project. 2011 Reed Graduate. Quinn Langdon. Hybe and go Seq: application of genomic tools to sociogenomic questions in the cichlid genus Julidochromis. ... The technical obstacle that arises for direct comparison between species is that one must first verify that genomic DNA sequence differences are not confounding the expression difference that one aims to measure with microarray analysis. A concern with our heterologous hybridization technique is that underlying genomic sequence difference could bias the results.
24 January
LSUHSC School of Medicine | DNA Microarray References
DNA Microarray References. Reviews. Schena M Genome analysis with gene expression microarrays. Bioessays 18:427-431, 1996. Kozian DH, Kirschbaum BJ Comparative gene-expression analysis. Trends in Biotechnology 17:73-78, 1999. ... Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G Making and reading microarrays. Nature Genetics 21:15-19, 1999. Baldwin D, Crane V, Rice D A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants.
10 January
Computer vision methods for DNA | Prepare DNA microarray.
Imager for DNA | 2.3 DNA Microarrays
Other fabrication techniques for DNA microarrays utilize photolithography and electrochemical processes. Appendix A explains the dierent DNA microarray manufacturing techniques. DNA microarrays come in various spatial congurations ranging from a high-density array of spots to a low-density array. ... The Cy3 dye has an advantage over Cy5 dye of improved resistance to ozone degradation [30]; as a result, it was selected for this setup because the lab does not have ozone reduction equipment.
DNA Microarray Placement For Improved Performance And
DNA Microarrays or DNA chips have become a standard method for identication of DNA sequence (genes or gene mutation), determination of abundance of genes and other genomic analysis. DNA Microarrays are composed of small DNA fragments (probes) which are manufactured using masks and photolithographic method similar to VLSI industry. ... We pro-pose a new cost-metric based on thermodynamic stability to account for hybridization potential of DNA Microarrays. Further, we propose a Hilbert-curve lling technique based method for thermodynamic stability based placement for-mulation...
Experimental and computational applications of
An assessment of the level of microarray technology in Africa, its availability and techniques required for malaria eradication and effective healthcare in Nigeria and Africa in general were also underscored. Key words: Malaria, microarray, Gene expression profile, Plasmodium falciparum, RNA. INTRODUCTION A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is defined by Wikipedia encyclopedia as a collection of microscopic DNA spots, commonly representing single genes, array-ed on a solid surface by covalent attachment to chemi-cally suitable...
Areas of Study and Courses | UCSC Extension Silicon Valley
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Links to the page contain: DNA Microarrays: Principles, Applications and Data Analysis....
How many of you have checked out | Uses of DNA microarrays
DNA microarray technology. Cluster analysis or clustering is the assignment of a set of observations into subsets (called. clusters) so that observations in the same cluster. are similar in some sense. Clustering is a method of unsupervised learning, and a common technique for statistical data analysis used in many fields, including machine learning, data mining, pattern recognition, image analysis and bioinformatics. Besides the term clustering, there are a number.
Mechanics of DNA Microarrays
Constructing DNA Microarrays. § A DNA microarray is a collection of DNA probes separated in a regular array atop a solid support (glass slide, silicon chip, etc). § Affymetrix oligonucleotide microarrays • Short oligonucleotide probes (25mers) are synthesized directly on a silicon wafer using photolithography methods. • Multiple oligonucleotide probes per gene including mismatch probe controls. § cDNA microarrays • Full length cDNAs are PCR amplified and then printed using a robot onto coated glass slides.
Magnetic Scanometric DNA Microarray Detection
Biosensor chips based on magnetic sensor arrays have been proposed to create easy-to-use portable lab-on-a-chip devices that are sensitive, versatile and easily integrated with standard silicon integrated-circuit technology. In a typical magnetic array chip, underneath each magnetically-labeled DNA spot sits a magnetoresistive (MR) sensor, using either giant magnetoresistive (GMR), spin valves or tunnel junction sensor designs ... Quantification of the measured magnetic field from each spot was carried out via image processing techniques analogous to those used in the analysis of fluorescent microarrays.
Signal Processing for Real-Time DNA Microarrays
Vikalo, Haris and Hassibi, Babak and Hassibi, Arjang (2007) Signal Processing for Real-Time DNA Microarrays. In: Conference Record of the Forty-First Asilomar Conference on Signals, Systems and Computers, 2007. ... On the other hand, a novel technique (i.e., real-time microarrays) capable of recording the kinetics of hybridization in fluorescent-based microarrays has recently been proposed in [1]. The richness of the information obtained therein promises higher signal-to-noise ratio, smaller estimation error, and broader assay detection dynamic range compared to the conventional microarrays.
18 March
METU | Bioinformatics Graduate Program | Courses
This course will provide an introduction to bioinformatics. The computational techniques for mining the large amount of information produced by biological experiments such as genome sequencing, microarray technology, and other high-throughput experimental methods will be introduced. The main emphasis of the course is to provide an overview of the area and describe solutions to fundamental problems of bioinformatics such as DNA and protein sequence alignment, protein structural alignment, protein/RNA structure prediction, phylogenetic tree construction, microarray data analysis, and analysis of...
29 June
Comparing whole genomes using DNA microarrays
DNA microarrays present an alternative way to study differences between closely related genomes. Advances in microarray-based approaches have enabled the main forms of genomic variation (amplifications, deletions, insertions, rearrangements and base-pair changes) to be detected using techniques that are readily performed in individual laboratories using simple experimental approaches.
Lab 7 – Isolation of Chromosomal DNA from Bacillus licheniformis – Run chromosomal DNA on 0.7% agarose gel. Lab 7 write up due M 3/23. Pre-Lab 8 - PCR practice – amplification of the a-amylase gene – assemble PCR reaction mixes. ... Test One. Solution making & protein techniques. M7-15. Spring Break. W 225. Unit Two – DNA Techniques.
30 April
Microarray technology for space exploration.
...in situ resource utilization (ISRU) and techniques for purposes of life detection (LD) and. ... This team includes the Lab-on-a-Chip Applications and Development (LOCAD) ... In regards to those generally termed "genotyping" applications, DNA microarrays may be...
Fatal error: 'break' not in the 'loop' or 'switch' context in...
Links to the page contain: Microarray Analysis....
14 August
Genomics Shared Resource | University of Colorado Cancer...
The Genomics and Microarray Shared Resource at University Of Colorado Denver Cancer Center is an advanced, state-of-the-art DNA and Protein microarray and Next Generation (NextGen) DNA sequencing technology center providing crucial research support for investigators interested in using ... • Single Cell Genomics: • Fluidigm C1, BioMark HD, Juno, and AccessArray. Our team is dedicated to providing high-quality microarray and NextGen DNA sequencing laboratory instruction, service, and consultation to the research and clinical community affiliated with UCDenver and other research institutions in the...
6 April
Oligonucleotide microarray identification of Bacillus anthracis...
7 FUTURE WORK. One of the objects of exploring new microarray data analysis techniques is to reduce the number of microarray replicates that are required to quantitatively discriminate between closely related strains at a known level of statistical condence. The results pre-sented here, using a gel element array format for microarray-based DNA ngerprinting, combined with previous data using planar microarrays, provides the opportunity to quantitatively compare microarray substrates...
14 April
Course Description | Advanced Academic Programs
Johns Hopkins University Zanvyl Krieger School of Arts & Sciences Advanced Academics Programs 202-452-1940.
8 December
Microarray-Based Research | Measure level of DNA expression
Neuroscience & Physiology and Psychiatry Center for Neuropsychiatric Genetics SUNY Microarray Core Facility Upstate Medical University Syracuse, New York. What is a microarray? • A patterned grid of biological material fixed to a solid surface. – DNA or RNA – Protein/antibodies – Tissue – Colonies (e.g., bacterial or yeast). What microarrays let you do. • Measure level of RNA expression.
DNA Microarray Image Intensity Extraction Using Eigenspots
Image and Video Processing Laboratory The Katsaggelos Lab. ... Abstract. DNA microarrays are commonly used in the rapid analysis of gene expression in organisms. Image analysis is used to measure the average intensity of circular image areas (spots), which correspond to the level of expression of the genes.
21 August
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3 April
Director, DNA Microarray Core Facilty Research Associate...
Dr. Sridar Chittur. Director, DNA Microarray Core Facilty Research Associate Professor, Dept. Biomedical Sciences School of Public Health. Academic Background. ... My lab in collaboration with the Tenenbaum lab developed the application of RNA immunoprecipitation to Affymetrix microarrays (RIP-Chip). We have worked with many collaborators to apply microarray technology to profile gene expression and alternative splicing in a wide variety of biological systems.
17 March
Microarray expression proling: capturing
...as much upon good micro-bial physiology technique as they do on good DNA array technique. ... compared with exponentially growing planktonic cultures in rich lab-oratory media. ... D. (1999) A comparison of gel-based, nylon lter and microarray techniques to...
Ph.D Biomedical Genetics Lab Syllabus
Textbook supplies basic techniques. 2. Isolation and quantification of DNA, (Newman) - extraction of DNA from blood for future experiments. 3. Insertion/deletion analysis (Deborah Lyn) - use of primers, PCR and agarose gel detection of insertion/deletion mutations. 4. TaqMan SNP analysis (Newman)- use of TaqMan SNP probes and real ... 7. Microarray B (Leonard Anderson) – detection of gene expression using microarray analysis. Laboratory: Written exams - 50% each- Short answer questions about experimental design will be submitted by instructors to the course director. Final exam will be cumulative.
Microarray Technology
5. Expression profiling with DNA microarrays. cDNA “A” Cy5 labeled. ... Advantages • Lower price and flexibility • Can be printed in well equipped lab ... Manufacturing Process Solid-phase chemical synthesis and Photolithographic fabrication techniques employed...
Lab 9
fluorescence, antibiotic resistance, E. coli. INTRODUCTION: In this lab you will perform a procedure known as a genetic transformation. Remember that a gene is a piece of DNA that provides the instructions for making (coding for) a protein that gives an organism a particular trait. ... In the second lab period you will analyze your results. Part I : bacterial transformation. Exercise A: Introduction to Sterile Technique (in lab session).
Department of Biostatistics
Page Not Found. No page could be found at this address. Back to Home.
25 March
Dartmouth Genomics and Microarray Laboratory...
Phase II is the carrying out of the microarray experiment itself to generate the raw data, and we carry out preferred protocols covering RNA isolation and RNA quality control assays, RNA amplification, complementary DNA (cDNA) synthesis, cDNA and amplified RNA (aRNA) labeling, microarray slide production, microarray hybridization and wash conditions, and microarray slide ... What questions are you trying to answer? What type of tissue/cells do you plan to use? How easy or difficult it is to obtain quality RNA from your samples? What RNA isolation technique is appropriate for your chosen tissues or cells?
27 January
Audrey Sassolas, Be?atrice D. Leca-Bouvier, and Lo??c J. Blum
There are many techniques in bioinformatics for the analysis of DNA microarray data.421-423 For example, Affymetrix developed the GeneChip Scanner 3000, which is a 16-bit sophisticated opto-mechanical confocal scanner measuring fluorescence intensity emitted by the labeled cRNA bound to the probe arrays. ... 2001, 3, 74. (289) Farkas, D. H. J. Assoc. Lab. Autom.
Preparation of functional DNA microarrays through...
The rise of DNA microarrays marked an important step in the development of sensors allowing parallel and rapid detection and identication of genes and gene mutations for genomics and biomedical diagnostic applications. The need for the production of low-cost microarrays with high spots density, precision, and repeatability has resulted in extensive research devoted to the design and development of different arraying techniques, the most extended ones being photoli-thography, pin deposition, and ink-jet printing.1,2.
404 | The University of Virginia
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15 December
Provost's Learning Innovations Grant for Faculty
The most widely used technique for the analysis of gene expression on a global scale is DNA microarray analysis. ... Teaching this course poses many challenges. First, many students have a fear of statistics and would rather be out in the biology lab doing experiments to obtain data from a microarray rather than sitting in class learning about estimating the intensity of the signal from the scanned images and analyzing complex genetic information.
Hybrid swarm negative selection algorithm...
E. Bura and R. M. Pfeiffer, Graphical methods for class prediction using dimension reduction techniques on DNA microarray data, Bioinformatics 19 (2003) 1252–1258.; 11. Ramaswamy S., Tamayo P., Rifkin R., Mukherjee S., Yeang C.H., Angelo M. Ladd C., Reich M., Latulippe E., Mesirov J.P., Poggio T., Gerald W., Loda M., Lander E.S., Golub T.R., Multiclass cancer diagnosis using tumor gene expression signatures, Proc.
2 April
Schedule of Classes - Sections
Topics to be covered will include photolithographic techniques for high-density DNA microarray production, incorporation of CMOS control into electronic DNA microarrays, direct electronic detection technology used in microarrays and biosensor devices, and focus on problems related to making highly integrated devices (lab-on-a-chip, in-vivo biosensors, etc.) from heterogeneous materials and components.
24 March
The contents of this course include introduction to molecular genetic lab, solution preparation methods, DNA isolation in plants, determination of DNA quantity and quality, PCR, preparation of agarose and polyacrilamide gel, the use of biochemical markers in breeding, hybridization-based molecular techniques and practices used in horticulture breeding, determination of gen expression (cDNA-AFLP, microarray), quantitative determination of gene expression (Real Time PCR)
Basic Steps t With mRNA degraded reverse cDNA cre Microarray Every spot on the chip represents a different coding sequence from different genes. Eac Basic Steps t Incubation with the mixed cDNA and the chip DNA will yield some pair Visualizing The slide with the microarray chip is placed inside a dark box where it is scanned with a high resolution laser Analyzing Creates a ratio image. ... Microarray works as reverse hybridization method converting from mRNA to cDNA 3’-5’ with TTTT…end. Probe – an attached nucleic acid with a known sequence (the DNA chip).
Microarray data analysis
A microarray is a collection of small DNA spots attached to a solid surface. In microarray experiments, the signal collected from each spot is used to estimate the expression level of a gene. A microarray contains thousands of DNA spots, covering almost every gene in a genome. o The first high-throughput technology for gene expression analysis. o Emerged in late 90s.
13 February
Development of a Novel DNA Microchip for
ABSTRACT Although DNA microarray can detect multiple DNA samples simultaneously, current detection techniques involve PCR and other traditional procedures. In this study, a sensitive, specific and rapid detection method, which eliminates PCR and other lengthy processes, for pathogenic DNA is presented. ... Also, I would like to thank all the lab members for being very supportive, friendly and helpful.
New Page 2
• Today DNA can be extracted and isolated from any type of cell and biological material, but different types of cells (e.g. bacteria, plant cells, animal cells) require slightly different extraction techniques depending on their size, cell membrane composition and cell surrounding structures, e.g. cell walls or other protective layers. The very simple procedure you will learn in the first part of this "DNA Isolation" lab enables the extraction of DNA from most types of plant cells.
19 March
Bacterial genomics: the use of DNA microarrays and
As the number of completely sequenced microbial genomes is increasing, functional and comparative genomic techniques will be employed for sequence analysis and gene characterization. Sequence comparison and expression profiling by DNA microarrays can determine phylogenetic relationships and identify genes while bacterial artificial chromosomes (BACs) allow the study of entire biochemical pathways and permit the expression of bacterial genes in a foreign host.
Introduction | Reading DNA
anatomy & dissections; cardiac punctures for blood collection § Analytical Techniques: Bradford-Lowery Protein Assays, SDS-PAGE Gel Electrophoresis, Titrations, Column. Chromatography, Western blotting, Radioligand Competitive Binding Assays, Quantitative Real-Time PCR Multiplex. Assays, Reverse Transcriptase PCR, Glycobiomarker Arrays, DNA & Protein Microarrays, Bomb Calorimetry § Lab Safety & Management: General safety in BL2 & BL3 labs; general lab inventory management; operation of flow.
Sequencing and Genomic Technologies | Duke GCB
DNA Sequencing. ... The Sequencing and Genomic Technologies Shared Resource is a basic research oriented core facility affiliated with the Duke Cancer Institute (DCI). This Shared Resource was created by the merger of two existing Duke Center for Genomic and Computational Biology units: The Microarray Core Shared Resource and the Genome Sequencing Shared Resource.
22 February
Microarray Core - Home
>> DNA Array Core. >> Microarray Core - Home. Overview Faculty. ... The Scripps Research Microarray Core Facility was established in 1998 to provide microarray technology to the Scripps research community. The core provides full service, including sample preparation, processing, biostatistical analysis and bioinformatic support. Services.
20 March
An Overview Of DNA Microarrays: From Technology To...
Expression Microarray Technology. DNA microarrays, also called Gene Chips, are tools for studying gene dynamics in a highly parallel fashion. In simplest terms, they are ordered collections of DNA sequences (probes) deposited on – and chemically bound to – solid surfaces (like microscope slides) or three-dimensional matrices. ... Many studies have compared microarray-derived expression levels or ratios with expression levels/ratios determined by more quantitative mRNA assessments, such as quantitative or real-time PCR techniques.
Description: Molecular genetics, classical experiments on DNA, Replication and transcription, types of DNA replication, RNA splicing , Gene variants, Translation, Regulation of gene expression- lac and trp operons, Recombina nt DNA technology, DNA cloning, techniques for screening libraries with clones, Northern, Southern and Western Blotting and PCR, applications of ... The faculty conducting the Laboratory will prepare a list of 12 experiments and get the approval of HoD/Director and notify it at the beginning of each semester. Credits: 0:0:2. 15BI3009 microarray data analysis lab.
BIO 107 Lab # 8: Summary & Study guide
This lab did not involve setting up experiments to study or investigate certain concepts/phenomena as you have done so far; rather it was a “techniques” lab. You learned 2 new techniques: how to isolate the giant polytene chromosome from Drosophila (fruit fly) and stain it; and how to extract DNA from onion. You will use the extracted DNA for gel electrophoresis later on in lab 8.
Main components of microarrays: (1) Hybridization (2) The ability to attach a known DNA molecule to a solid surface. Expression: To measure RNA (1) Convert RNA to DNA (2) Measure DNA This is a common trick: to measure X in a cell, convert X to DNA and measure DNA. Microarray: basic idea. We try to measure a specific (short) DNA sequence called “the target”, which we measure using “a feature”. (1) Take a known DNA sequence and attach many single stranded copies in a specific place on a solid surface.
Dna extraction lab
You can usually get more DNA to precipitate from the solution by using one of the DNA-collecting tools (such as a glass or paper clip hook) to gently lift the water solution up into the alcohol. This allows more DNA to come in contact with the alcohol and precipitate. You may find it helpful to pour the water/detergent solution into a clean test tube, leaving behind the wheat germ, before adding the alcohol. What is DNA?
6 February
Genome Probing Using DNA Microarrays
In microarray technology, DNA hybridization is turned upside down. Instead of the target DNA being fixed to a substrate, such as a filter in Nothern and Southern Blots, and a labeled probe applied, the probe is fixed and a labeled pool of DNA or cDNA molecules is applied. In the example shown in Figure 9.3 the microarray contains Expressed Sequence Tags (ESTs), cDNAs corresponding to expressed genes. (You are cloning ESTs from Arabidopsis.) The technique can be used to determine what genes are turned on in response to serum.
12 November
Cluttered Scatterplot Matrix. Projection Pursuit Techniques. 1-Dimensional Visualization. Parallel Coordinates. ... Heatmap. • After Sort to find groups. Example: DNA Microarray. • DNA Microarrays are small, solid supports onto which the sequences from thousands of different genes are immobilized, or attached, at fixed locations.
Pre-lab Homework Lab 3: DNA Structure and Function
OBJECTIVES: After successfully completing this lab, a student will be able to: • Describe the structure of DNA and how this structure allows replication. • Demonstrate the processes of DNA replication, transcription & translation • Explain how changes in DNA structure can cause changes in protein structure. ... The goal of this laboratory exercise is for you to see, touch and feel DNA. Scientists in biotechnology and research laboratories perform essentially the same technique you are performing today to purify and study DNA. How This Procedure Works
Attach fluoresce Competitive Hybridization Dot color indicates presence/absence of mRN My Prop Flow Cytometer Microbeads Fluo Project O Test new method for use of microarrays find suitable beads stick DNA to bead Work Co Familiarized with microarrays Researched microb Curren Analyze Raman Spectroscopy of beads inelastic scattering technique probe vibr Futur Work to attach DNA to beads Hybridiz.
PREPARED BY | Figure 3: Single channel microarray image [7]
CVIP Lab University of Louisville Electrical and Computer Engineering. ... Microarray imaging is a very powerful technique to study the gene expressions, understand the interactions between ... 2001). DNA Microarray Methodology - Flash. Animation. Available
Genetics Laboratory - The University of Oklahoma Health...
Convential Molecular genetic techniques allow us to detect changes of as little as one base pair of the DNA sequence, however the target area or gene has to be identified in advance to make this possible. Microarrays combine the assets of both conventional molecular and cytogenetics to allow a whole genome screen to be performed but with the ability to detect changes smaller than 5Mb. ... Ask The Genetics Lab.
1 June
Microarray in Endometriosis
Microarray in Endometriosis: Clinics to Research Laboratory. 3 – 7 November 2009. Program. Blastocyst Implantation Biology Laboratory Department of Physiology. ... Tuesday, ovember 3, 2009 Initiation of Wet Lab Experience Seminar Room, Department of Physiology All India Institute of Medical Sciences (Only for the Registered Participants). 2.30 pm Endometriosis – Molecular Strategy: Interactive Session. Professor D. Ghosh.
Pages · Towson University
24 April
New Page 3
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Links to the page contain: A numerical Comparative Study of Various Flooding Techniques in......
19 August
The Structure of DNA
DNA is made up of six smaller molecules -- a five carbon sugar called deoxyribose, a phosphate molecule and four different nitrogenous bases (adenine, thymine, cytosine and guanine). Using research from many sources, including chemically accurate models, Watson and Crick discovered how these six subunits were arranged to make the the structure of DNA. The model is called a double helix because two long strands twist around each other like a twisted ladder.
20 October
DNA Hybridization Detection
High density DNA Microarray. DNA microarrays, Oligonucleotide arrays, GeneChip arrays, DNA chips are all similar terms Revolution in the analysis of genetic information Hybridization is a highly parallel search by each molecule for matching partner on an affinity matrix. Specificity and affinity of complementary base pairing. Use of glass as a substrate, fluorescence for detection and the development of new technologies for synthesizing or depositing DNA have allowed the miniaturization of DNA arrays with increases in information content.
Microarrays: branching out from expression analysis
Chromatin immunoprecipi-tation (ChIP), an assay used to detect inter-actions between proteins and DNA, has been combined with DNA microarray technology in a method dubbed ChIP-on-chip or loca-tion analysis. In this technique, a protein is cross-linked to DNA upon binding. ... One of the biggest bottlenecks in making carbohydrate microarrays is synthesizing the actual carbohydrates, a laborious and expensive process, out of the reach of most academic labs. Additionally, one of the limitations of the technique is that there is no way of knowing how much sample is bound at each spot.
A fuzzy k-nn approach for cancer diagnosis with microarray
Recent advances in DNA microarray technology have made it possible to measure the expression level of several thousand of genes simultaneously. The gene expression profiles obtained from microarray techniques have provided the opportunity of early diagnosis of cancer with the use of supervised learning algorithms. ... Additionally, the DNA microarray technique allows measuring rapidly and simultaneously a great number of genes in different tissue sample.
Unit - University of Canberra
Links to the page contain: Contemporary Leadership Techniques (9200) - 3 cp, Level 3....
1 September
3. DNA Microarrays
Bead-based microarrays are an alternative format of planar arrays [12]. Protein microarrays were urged as a technique to exploit the worthy knowledge of nucleic acids array methods. Hence, a brief review of DNA microarray technology is provided in this chapter. ... 46. interferon-gamma and tumor necrosis factor-alpha,” Clin Chem Lab Med 40 (5), 509-519 (2002). 56. W. H. Robinson, C. DiGennaro, W. Hueber et al., “Autoantigen microarrays for multiplex characterization of autoantibody responses,” Nat Med 8 (3), 295-301 (2002). 57. V. Knezevic, C. Leethanakul, V. E. Bichsel et al., “Proteomic profiling of...
Separation of Mixtures Using Different... : Amrita Online Lab
Used in diagnostic laboratories for blood and urine tests. Used in dairies and home to separate butter from cream. Used in washing machines to squeeze water from wet clothes. ... Learning outcomes. Student understands the following terms: solvent extraction, chromatography, RF , centrifugation, simple distillation, fractional distillation, etc. Student acquires skills to perform experiments using the following techniques in the chemistry lab
30 September
Restructured curriculum phase IV
1 Stem cell Technology 2 Separation techniques for Bio molecules 3 r-DNA technology 4 Separation Techniques for biomolecules - Lab course 5 r-DNA technology - Lab course. ELECTIVE SUBJECTS(ES) PAPER Applied Electronics in instrumentation Science/ Therapeutic drug monitor (Not more than 2 papers at a ... Cell surface analysis of proteins using fluorescent dyes. Stem cell technique. Unit V: dna diagnostic systems. Hybridization probes,PCR, DNA fingerprinting, DNA Microarray, FISH Technique, Molecular diagnosis of genetic diseases.Biothesiometric technique, Auto analyzer, LASER.
Microarray-based whole-genome
The practice of DNA–DNA hybridiza-tion has allowed the establishment of a relatively stable and operative classification system for pro-caryotes (Stackebrandt et al., 2002). Over the last 50 years, various hybridization-based techniques have been developed for microbial taxonomy (Rossello-Mora, 2006). ... Compared to the conventional nucleic acid hy-bridization with porous membranes, real-time PCR and other molecular approaches, microarray-based hybridization offers advantages of high-throughput and parallel detection. DNA microarrays have been widely used to analyze gene expression in...
Summary of DNA Microarrays data analysis - 2006
Introduction. This course is targeted to students in biology or biochemistry who are interested in the DNA chips and microarrays technologies. The aim of this course is to familiarize graduate students with the DNA microarray technology and with the analysis of gene expression data (including a tutorial on R: a language and environment for ... Course objectives. To ensure familiarity with the different microarray techniques and their everyday use in a biological laboratory setting. To acquaint the students with the widely used "R" language and environment for statistical computing and graphics.
28 January
MRSA Research Center : Laboratory Research | Microarray...
For Laboratory Researchers – Microarray Technology. About Our Lab Research. ... Using a technique known as "fingerprinting," we can readily distinguish the traditional healthcare-associated MRSA strain from the new epidemic community-associated strain. We have found that this new strain of MRSA (called "USA300") has a genome pattern (called a "fingerprint") that is distinct from the previously more common strain that mainly affects people with healthcare-associated risk factors.
16 July
Carnegie Mellon Press Release: December 8, 2005
DNA microarray analysis—a multimillion-dollar-a-year industry—identifies gene activation in living, complex biological systems. DNA microarrays monitor the behavior of thousands of genes over time by detecting changes in the expression of as many as 30,000 different genes on one small chip. The technique has been used to study some of the most important biological systems, including how cells normally divide (the cell cycle) and immune responses to disease and infection.
8 December
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13 December
Chemistry Lab Techniques HomePage
Soon to be the home of the Chemistry Lab Techniques Home Page.
10 April
Microarray data analysis
A sample experiment with input and output files is also described for basic steps in “microarray data analysis”. You can modify the procedure to fit your own analysis; however, it may require additional software packages, techniques, and programming to analyze more complex experiment which will not be described ... Produce R package limma (linear models and differential expression for microarray data) and associated user-interfaces limmaGUI and affylmGUI. Wong Lab (Harvard University). DNA-Chip Analyzer. Yang, Jean (University of Sydney). R packages marray, DEDS and stepNorm.
Realtime Processing of a 2 MB Spotted Microarray (DNA Chip). Please drag a region to zoom-in.
14 January
Biotechnology (BIT) | BIT 567 Pcr DNA Fingerprin 2.
Theory behind laboratory techniques and overview of cloning strategies starting from nucleic acid or protein sequence data. Laboratory sessions involve subcloning, preparation of competent cells, transformation, screening recombinant DNA by colony hybridization and PCR, SDS-PAGE of recombinant protein, affinity purification, and western blots. ... At the conclusion of this course, students should feel comfortable with microarray experimental design, its tools, an analysis of generated data. This is a half-semester course. Student must register for both lecture and lab sections.
9 July
Practical Exercises in Microarray Data Analysis
Practical analyses of microarray data. This web contains links to different exercises and labs that I have taught along the time using different software tools and datasets. Although, at the moment, it is somewhat heterogeneous I have found it interesting to combine them in order o highlight what can or can't be done with each tool (of course it often means what the time, or the knowledge allowed to do or not to do).
26 February
DNA chip technology in the study of
The advent of DNA microarray technology has ushered in an era of systems biology whereby researchers can study the transcriptional behavior of thousands of genes in parallel. Advances in manufacturing techniques and informatics, and the availability of several genome sequences have furthered these capabilities to the point where whole-transcriptome studies can be accom-plished in yeast, ies and plants, and soon will be pos-sible in mammals.
Themagic | dna microarrays
Scientists rely on DNA microarrays for two very different purposes. So-called genotype applications compare the DNA on a chip with DNA in a tissue sample to determine which genes are in the sample or to decipher the order of code letters in as yet unsequenced strings of DNA. ... Several techniques that do not involve mi-croarrays can reveal the jobs performed by newly discovered genes (or, more. AN AORFRACYOMPANIES. The following are just some of the companies that sell or are developing array-related products and services: DNA MICROARRAYS.
DNA microarray technology – here the filters (membranes) have been replaced by a microscopic slide chemically-treated (e.g. nitrocellulose coated microscopic glass slides). Two type of microarrays depending on how the nucleic acid samples were generated and delivered to the microarray: - microarrays of pre-synthesized nucleic acids – individual DNA clones or oligonucleotides are spotted at individual locations (x, y coordinates of a miniaturized grid) using a robote.
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7 October
Analysis Techniques for Probe-level Microarray Data
Probe-level data Introduction Methods Results Conclusions. Future work Motivation Methods Preliminary results. Transcription factor, known to regulate gene expression Plays important role in memory formation Binds to a DNA element called cAMP-response element (CRE) We will use this gene as an example of a canalyzing gene. ... 2008. 2009. Extrachromosomal DNA. Analysis Techniques for. Probe-level Microarray.
Stony Brook University DNA Microarray Core Facility
John Schwedes. Basic Science Tower Level-5, Rm 151. SUNY Stony Brook NY...
10 December
Image gallery | microarray facility mission
The UVM DNA Microarray Facility was initiated by the Vermont Genetics Network in collaboration with the Ver-mont Cancer Center and the College of Medicine. ... Please submit a Target Prep order form using your iLabs Account. The following information is required: Sample ID, RNA/gDNA Concentration (ng/uL), Origination Source, Isola-tion Technique, and Array Chip to Run. The concentration of RNA samples should be adjusted to 20ng/uL in nuclease-free water, with a 10uL volume submission.
"Automated liquid dispensing pin for DNA microarray..."
In particular, the application is focused on DNA microarray fabrication with the goals of smaller spot size, higher yield, more efficient usage of biological materials, and capability to handle high viscosity liquids. The new system is based on active sensing and control and it is part of a fully integrated robotic microarray system for genomic and proteomic applications. The prototype system handles water as well as thick liquids such as 100% glycerol and generates spots in a contactless manner with controllable spot size ranging from 80 microns to 200 microns.
20 August
Protein microarray technology | Technique
DNA microarrays are used for genetic analysis as well as expression analysis at the mRNA level. ... The most promising approaches in this field are phage-display techniques [16,17] combined with highly diverse (up to 1011 independent clones) ... Clin. Chem. Lab.
Molecular Techniques | Microarrays
Lecture & Lab Outlines. Other Stuff. daj's Home Page. ... Northern Blotting, Southern Blotting, Western Blotting: These techniques combine electrophoresis and hybridization of specific probes to identify DNA present in a sample. Microarrays.
3 February
Helmann Lab | Department of Microbiology
Helmann Lab. The difference between what an organism can do (genetic potential) and what it actually does (phenotype) is often regulated at the level of transcription. Our laboratory studies Bacillus subtilis, a Gram-positive soil bacterium and genetic model system. ... Students in our laboratory can expect to gain experience in a wide range of techniques as applied to this model genetic system. Most research projects will include some or all of the following: genomics, e.g. DNA microarray analyses; computer-based approaches to defining regulons.
28 July
DNA, RNA isolation Cell Counting techniques. ELISA Computer comparison, management of DNA sequence. Concentration DNA Chips/Microarrays. Separation Immunoassay methods Agarose gel electrophoresis Toxicology testing & Bioassay. ... • Point-of-Contact Medical Diagnostic and Therapeutic Uses. When lab-on-a-chip (LOC) or microarray technology becomes fully realized, the hope is that doctors will be able to perform multiple lab functions (DNA preparation, sequencing, data analysis) on very small devices, in real time.
DNA Extraction Lab
DNA Extraction Lab. A complete copy of DNA is found in every cell in any organism. In order to release the DNA to analyze it, scientists must break open the cells and remove structural proteins and enzymes that interfere with the DNA structure. This procedure releases a great deal of DNA so that you can see it.
Small Molecule Microarrays
Akin to DNA microarrays, small molecule microarrays could serve as an essential research tool for the under-standing of the mode of action in various bioactive small mole-cules. To realize this potential in a research setting, the immobilization technology of small molecules on the surface of microscope glass slides has been a ... Another interesting application of the in situ methylation procedure described here is the possibility to probe the presence of antibodies directed toward methylated epitopes starting from easy-to-make and cost-effective unmodified peptide libraries and standard microarray techniques.
Gene-Expression Microarrays Classification using Feature...
The main data analysis techniques [4] used currently in biomedical applications related to microarrays are ... Applying machine learning algorithms on DNA microarray data sets is of maximum importance for ... The department will supply a small computer lab and Dr...
Ctgtgcaagcatgacgt gaattc gaggtcaacacatg
For this reason it is important for you to begin to gain experience with the basic fundamentals of molecular biology in the laboratory. One of the most widely publicized uses of molecular biology techniques is for the purpose of identification of criminals through what is commonly called Forensic DNA fingerprinting. ... You will also need to wear protective eyewear for some portions of the lab. We have goggles available for use in the lab, but if you would prefer to purchase your own, they are also available in the GRU Bookstore. DNA Fingerprinting Lab 1: Genomic DNA Isolation & PCR.
Bio 3A Lab: DNA Isolation and the Polymerase Chain Reaction
Analysis of the data generated in this laboratory will enable you to determine whether your genomic DNA carries this piece of DNA, or not. The genome, composed of DNA, is our hereditary code. This is the so-called "hard-wiring", the blueprint that controls much of why we look like we do, why we act like we do, and how we do the things we do. ... Before PCR, the molecular biology techniques used to study DNA required such a high level of expertise that relatively few scientists could use them. Bio 3A Lab: DNA Isolation and PCR 1.
Mining Frequent Patterns from Microarray Data
DNA MICROARRAY DNA microarray technology is an advanced technique to study gene expression in different conditions like drug treatment versus control or healthy versus disease conditions. DNA microarray technology is based on hybridization of DNA or oligonucleotide probes which represent specific genes with fluorescently or chemiluminescence-labeled DNA or cDNA fragments. Tens of thousands of DNA or oligonucleotide probes covalently bound to glass...
Answer Key for Strawberry DNA Lab
All the foods we eat that come from plants and animals that contain DNA. DNA has been consumed on a daily basis since the beginning of time and is completely safe to eat. 7. Look at the plant cell pictured on page one of the lab handout. Remember that genes are found on chromosomes, and genes control traits. Give at least two examples of traits that are expressed in the strawberry.
Evaluation of microarray-based DNA methylation
RESEARCH ARTICLE. Open Access. Evaluation of microarray-based DNA methylation measurement using technical replicates: the Atherosclerosis Risk In Communities (ARIC) Study. Maitreyee Bose1, Chong Wu1, James S Pankow2, Ellen W Demerath2, Jan Bressler3, Myriam Fornage3, Megan L Grove3, Thomas H Mosley4, Chindo Hicks4, Kari North5, Wen Hong Kao6, Yu Zhang7, Eric Boerwinkle3 and Weihua Guan1*.
Statistics for Human Genetics and Molecular Biology
• array CGH: DNA Copy Number. • ChIP-chip: TF binding sites. 2. mRNA. • DNA microarrays: custom array, Aymetrix, Agilent, Illumina. • SAGE. 3. Proteins.
BIO304: Forensic DNA Fingerprinting Lab
With the development of newer, more efficient DNA-analysis techniques, RFLP is not used as much as it once was because it requires relatively large amounts of DNA. In addition, samples degraded by environmental factors, such as dirt or mold, do not work well with RFLP. ... Comparing the mtDNA profile of unidentified remains with the profile of a potential maternal relative can be an important technique in missing person investigations. In today’s lab we will be performing a modified RFLP analysis of DNA collected at a crime scene and comparing that with DNA isolated from various suspects.
Fact Sheet Describing Recombinant DNA and Elements...
Gene expression can be studied using microarray analysis, which is a method of visualizing the patterns of gene expression of thousands of genes using fluorescence or radioactive hybridization. ... DNA sequencing is a lab technique used to determine the sequence of nucleotide bases in a molecule of DNA. 4. Creation of transgenic plants and animals.
Arts & Sciences | Boston University | A Pioneering Technique
A Pioneering Technique. A protein-binding microarray is used to find which of the thousands of locations on the human genome particular proteins bind to. When these locations are pinpointed, they can be targeted by improved drugs to treat inflammatory diseases, such as arthritis and lupus. To identify where these two proteins are binding to the DNA, Siggers and his lab team use an impressive new instrument in the biologist’s toolbox: a protein-binding microarray.
13 June
John Frank Rakus, Ph.D.
Teach General Chemistry I lecture and lab; teach Biochemistry I ... Recombinant DNA techniques, mammalian tissue culture and transfection, western blotting, protein ... proteins. Techniques: Protein microarray design, fabrication and analysis, mammalian.
“Statistical Analysis of DNA Microarray Data”
Microarray techniques have been widely used to monitor gene expression in many areas of biomedical research. They have been widely used for tumor diagnosis and classification, prediction of prognoses and treatment, and understanding of molecular mechanisms, biochemical pathways, and gene networks. Statistical methods are vital for these scientific endeavors. In this talk, I will review recent developments of statistical methods for analyzing data from microarray experiments.
Courses | BIOLOGY 275 Recombinant Dna Techniques (6)
Laboratory course emphasizing hands on experience with molecular biological techniques utilized in modern research laboratories. Techniques include gene cloning, PCR, DNA and protein electrophoresis, and protein purification. ... BIOLOGY 286 Molecular Lab Techniques In Medical Diagnostics (2). Practical experience using molecular techniques, such as PCR and ELISA, for medical diagnostic assays. Emphasis will be placed on understanding theory, experimental design, interpretation of results, and the limitations of these assays.
1 December
Microarray Data Analysis
GRADING A written report about statistical analysis of a specific microarray dataset, and a PowerPoint (or equivalent software) presentation, are required. COURSE SCHEDULE Lecture 1 (1 hour) Microarray technologies Lab #1 (2 hours) Microarray Data acquisition Lecture 2 (1 hour) Preprocessing microarray data Lab #2 (2 hours) Lecture 3 (1 hour) Identifying differentially expressed genes Lab #3 (2 hours) Lecture 4 (1 hour) Annotation Lab #4 (2 hours) Multivariate techniques Lab # 5 (3 hours) Putting all together / assigned real microarray data sets.
Faculty of Engineering and Technology
Links to the page contain: Instrumentation & Measurement Techniques....
26 December
We emphasize hands-on experience with lab techniques applicable to addressing a variety of ... At the conclusion of this course, students understand microarray experimental design ... The haploid human genome occupies a total of just over 3 billion DNA base pairs.
CBI-Publications--DNA Microarray Design and Data Analysis
DNA Microarray Design and Data Analysis.
3 January
p53 Mutation analysis in breast tumors by a DNA microarray...
p53 Mutation analysis in breast tumors by a DNA microarray method. Shields, PG., Tennis, M., Krishnan, S., Bonner, M., Ambrosone, CB., Vena, JE., Moysich, K., Swede, H., McCann, S., Hall, P., & Freudenheim, JL. "p53 Mutation analysis in breast tumors by a DNA microarray method." Cancer Epidemiology, Biomarkers & Prevention 15.1 (2006): 80-5.
6 February
Methods | Quantifying the DNA
llWhat will be presented: experimental methods used for studying the molecular biology of cancer Goal of this class: Obtain an appreciation of practical application of molecular techniques llMolecular biology techniques utilize DNA, RNA, and enzymes that interact with nucleic acids to understand biology at a molecular level. ... SNP microarrays are DNA microarrays that are used to identify genetic variation in individuals and across populations.
Application of Stellar Photometry to the Analysis of...
DNA microarray technology allows for the simultaneous evaluation of genes that may be critical for the prevention and treatment of cancer. A critical step in the analysis of microarray data is the quantification of spots on the array platform. Insufficient attention has been given to the precision and accuracy of spot intensities.
DNA Extraction and Gel Analysis - EG1003
Describe the major techniques used in this lab: DNA Restriction, Gel Electrophoresis, etc. Important properties of DNA directly having an impact on the extraction procedure. Clearly describe the procedural steps the way they were carried out in lab. ... Team PowerPoint Presentation. Follow the presentation guidelines laid out in the page called EG1003 Lab Presentation Format in the Introduction to Technical Presentations section of this manual. When preparing the presentation, consider the following points: Rely heavily on graphics and pictures.
16 August
Uniformed Services University | Learning to Care for Those in...
Physiology: Microarray and Proteomic Data (Unpublished). Biochemistry: Metabolic Pathway. Resistance Phenotypes of Novel D. radiodurans Mutants (unpublished). ... Recent studies from several independent labs implicate protein damage as the major probable cause of death in irradiated cells. Whereas DNA lesion-yields in cells exposed to a given dose of radiation appear to be fixed, protein-lesion yields are variable and closely related to survival.
9 April
Biological References | DNA Structure
Nucleic Acids. • Two kinds: – RNA: ribonucleic acid – DNA: deoxyribonucleic acid. ... Polymerase Chain Reaction. In order to make enough RNA for microarray experiments, PCR is used to amplify the amount of RNA. Most PCR methods typically amplify nulceic fragments of up to 10 kilo base pairs (kb), although some techniques allow for amplification of fragments up to 40 kb in size.
...lab skills and safety -Lab notebook record keeping -Genetics Review: · DNA structure & function · Protein structure & function · Gene expression and regulation · Inheritance -Labs: DNA technology and analysis · DNA extraction · DNA analysis · Gel electrophoresis · Restriction Enzymes · DNA microarrays (simulated) ... Genetic Engineering · Biotech and agriculture · DNA Barcoding- Research -Labs · Recombinant DNA technology · Bacterial Transformation · Biomolecule purification (chromatography techniques) · ELISA · Protein profiles w/vertical gels · DNA purification · PCR · DNA Sequencing (barcoding)...
All Associates will receive a stipend increase after one year of tenure. Additional Information About National Institute of Standards and Technology (NIST). Prior affiliation includes direct full-time employment relationships with the laboratory. Research contracts with universities that provide support for graduate students or faculty who perform research on campus are not ordinarily considered to be disqualifying.
28 January
The Sydney eScholarship Repository: Choose Login Method
My Sydney eScholarship. Receive email updates. Edit Profile.
10 September
Welcome to BIOL 572
Welcome to BIOL 572: Recombinant DNA techniques. Agenda 1: Introduce yourselves. ... DNA microarray analysis. Agenda 2: Course introduction. Lecture 1: 6 Fall 2006. ... Homework and lab reports are due Next Monday. Agenda 3: Some logistics for BIOL 572.
Union County College
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21 May
CCCWFU Microarray Core Facility
RNA samples that do not meet these quality/purity requirements may or may not generate adequate microarray results. If the investigator wishes to proceed with such samples, the array lab cannot be held responsible for suboptimal microarray results. Please note that it is also the investigator’s responsibility to collect the resulting microarray data from lab personnel within 2 weeks of being notified of completion of the project.
DNA Microarrays and Computational Analysis of DNA...
In this endeavor, it is important to keep in mind the abundance of already existing statistical and machine learning methodologies which can serve as the starting point for developing more specialized techniques. Here we describe different uses of DNA microarray technology in molecular carcinogenesis research and related methodological approaches for analyzing and interpreting DNA microarray data obtained in such experiments.
University of Maryland Libraries
Staff Directory. Circulation, Reserves, Billing & Interlibrary Loan. Technical Support. Suggestions.
15 December
Welcome to the LCCC Genomics Core! — Lineberger...
Both techniques are highly useful and the choice should depend on the exact goals of the research. We strongly recommend that you consult with the lab at the earliest stage of planning your study so that we can assure that you are using the best approach to meet your objectives. ... Gene dosage using comparative genomic hybridization (CGH). Using direct labeling method, 2 color separately labeled sample genomic DNA and reference genomic DNA hybridize on a same microarray.
10 February
Microarray Meta-Analysis Tool (MMAT)
METHODS The modeling of gene co-expression and regulatory net-works requires several steps that have their own technical challenges. The Microarray Meta-Analysis Tool (MMAT) uses techniques developed over the course of the rst author’s Master’s Thesis work [7]. A. Microarray Combination A DNA microarray, also commonly known as a DNA chip.
Core Laboratories and Facilities | Science and Engineering...
The facility provides equipment and training for DNA microarray handling, Western blot/gel/microarray scanning, PCR amplification, and analysis of DNA, RNA and protein samples. ... The lab is committed to generating high-quality, high-precision data with a state-of-the-art mass spectrometer and peripheral support devices. The lab also continues advising UNLV faculty and students on sample preparation techniques and on specific analytical requirements and method development.
16 September
NSW HSC Online
Exam material and other resources to help you succeed in your HSC. A Charles Sturt University (CSU) initiative developed in collaboration with the NSW Department of Education, Science and Training.
16 December
Lecture | DNA Microarray – Comparative Hybridization
Examining Biological Networks. X Indirect approach. 0 Measure mRNA production (gene expression) in cell O Random ESTs O DNA microarray. 0 Advantages O High throughput O Can test large variety of mRNA simultaneously. ... O Need to examine data O Look for large gaps between data 0 Handling large multidimensional data sets O Dimension reduction O Visualization techniques 0 Handling noise in data O Robust metrics for calculating.
PBRC GCF Microarray Analysis
How do you intend to analyze and interpret your array results (a lab technician, a statistician, yourself)? ... Most causes may be avoided through careful laboratory technique or can be corrected ... Missing value estimation methods for DNA microarrays.
12 December
Laboratory Resources - Rat Genome Database
Laboratory Resources. This page lists some possible sources for various research materials. If you would like to see a category that isn't included here, if you have suggestions of other sources for these or other types of materials or if you represent a company and would like a link to your site included in this list, please contact us and let us know. ... Antibodies. DNAs, RNAs and Related. Microarrays. Chemicals for Biomedical Research and Diagnostics.
7 July
Microarrays for the Detection of Bovine Pathogens
Also, all microarray experiments can be run using the same repeatable techniques ... reliable and consistent commercial arrays, though research labs still commonly produce ... Here we report on the design and evaluation of a simple DNA microarray used for the...
Diagnostic molecular pathology: current techniques and
During annealing, or hybridization, oligonucleotide primers bind to their comple-mentary bases on the single-stranded DNA. Finally, during polymerization, the polymerase enzyme reads the template strand and matches it with the appropriate. Molecular diagnostic techniques. ... Figure 11. (a) A computerized DNA microarray reader displays fluorescence intensi-ties at the different cDNA intercept locations. In this example, the gene indicated by the yellow arrow is markedly overexpressed in comparison to the genes in blue. (b) Variations in gene expression help identify patterns that may predict prognosis...
Applications of Biotechnology II | Microarrays
It also forms the basis of DNA fingerprinting techniques and has been used to perform genetic screening for the presence of mutations related to genetic diseases. Agarose is a seaweed extract available in powdered form. The powder is mixed with buffer, heated to dissolve the agar, poured in a mold, and allowed to cool. ... This procedure is used for DNA fingerprinting, DNA sequencing, construction of DNA probes, the diagnosis of genetic abnormalities, identification and classification of bacteria, and the detection of viruses. For a more brain numbing PCR animation go here. Microarrays.
5 April
Because this method does not detect unmethylated cytosines, a failure to detect a CpG region of interest could be due to its hypomethylated state or a technique problem in the purification process. ... Five 385K DNA Methylation microarrays were purchased from Roche NimbleGen to hybridize 2 undiff DNA samples, 2 diff DNA, and 1 A? DNA. Following quality control requirements by Roche NimbleGen for human DNA, all samples were amplified to and purified to achieve a final mass of at least 4 µg of DNA and a concentration of at least 250 ng/µl.
Center for Biofilm Engineering - Center for Biofilm Engineering
Conferences & Workshops World Wide. Job Opportunities. Lab Safety and Information. Speaker Guide.
9 September
Education in Russia for Foreigners: Study in Russia - Russian...
Specialist's programme: 070601 TV and cinema production 070301 Acting technique. Post-graduate course: 05.25.03 Library science, bibliography science and book science 05.25.05 Information systems and processes 09.00.03 History of philosophy 13.00.02 Theory and principles of training and education (music) 13.00.05 Theory, principles and organization of social and cultural activity 17.00.09 Theory and history of arts 22.00.06 Sociology of culture.
23 December
Dna microarray classification
Dna microarray classification. • Cancer. • Infection, radiation • Altered genes • Uncontrollable cell growth. ... • Is a cell malignant? • What kind of malignancy? Dna microarray classification. • Gene expression. • DNA -> Protein • Influenced by external factors such as diet.
Intro to DNA Microarrays
Intro to DNA Microarrays. Judy Wieber. BBSI @ Pitt 2007 Department of Computational Biology University of Pittsburgh School of Medicine. May 25, 2007. Also called. ? DNA chips ? biochips ? gene chips ? gene arrays ? genome chips ? genome arrays. ... ? An arrangement of DNA sequences on a solid support ? Each microarray contains thousands of genes ? Able to simultaneously monitor gene expression levels. in all these genes ? Used for: - gene expression studies - disease diagnosis - pharmacogenetics (drug discovery) - toxicogenomics.
Inactive Content
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15 December
MICROARRAY PROTOCOLS. cDNA Synthesis Protocol with Genisphere 900MPX Kit Revision September 2 2008. **NOTE-do cDNA synthesis protocol in RNase-free zone and remember to use Nuclease-free water only! ... Terminal Deoxynucleotidyl Transferase Tailing reaction. 1. To purified DNA a. Transfer all your purified cDNA (10 ?l) to a PCR tube. Do each sample separately. b. Add nuclease Free water to bring final volume to 16.5 ?l. 2. Heat cDNA in thermalcycler a. Heat for 10 minutes at 95?C b. Immediately transfer to ice for 2 minutes.
Microarray technology
An array of oligonucleotide of 20 80-mer oligos (small, endonuclease-produced fragments of 20 80 nucleotides) or peptide nucleic acid (PNA) is synthesized in situ (on-chip) by chemical synthesis techniques similar to photolithographic (light mask) used to make VLSI silicon chips. DNA Microarray by Spotting or printing (Patrick Brown, Stanford). An array of cDNA (complementary or copy DNA) is pre-synthesized from the RNAs of the organisms under study by reverse transcription (with an enzyme called DNA polymerase).
6 May
Microarrays Identied a Single Association with Inammatory
Both targeted gene methylation44 and DNA methylation microarray45 assessments have detected numerous colonic mucosal associates of inammation in IBD. Techniques with higher resolution may offer even more insight into the intestinal mucosal DNA methylation aspects of the disease group. In summary, our largely negative study can signi-cantly guide epigenetic investigations in IBD regarding technical planning and tissue selection.
Chain Reaction Method for Quantifying mRNA Levels
The participants learned to conduct microarray experiments and analyze microarray data. In the course of the workshop, the gel electrophoresis-based method used at Missouri Western State College for measuring complementary DNA (cDNA) levels was presented to the group and it generated a large amount of interest. ... 29(1), 23–39. Bustin, S.A., and Dorudi, S. (2002). The value of microarray techniques for quantitative gene profiling in molecular diagnostics. Trends Mol. Med.
and DNA Microarray Technology
An initial denaturation step of 3 min at 95°C was followed by 30 cycles of 30 s at 95°C, 30 s at 55°C, and 1 min at 72°C, then 5 min at 72°C. RNA was transcribed from these PCR-generated templates by using a commercial RNA transcription kit (New England Bio Labs Inc., Beverly, Mass.) in 150-?l. ... This study is the rst to compare the novel microarray technique and other methods, and it demonstrates that the target populations were qualitatively detected by mi-croarray hybridization. We anticipate that the DNA microar-ray technology used in this study will ultimately provide a rapid and high-throughput platform...
BOT 230 Biotechnology Laboratory I (DNA Techniques)
Biotechnology field, laboratory techniques, applications, and bioethical considerations. Metric system, solutions, spectrophotometry, bacteria culturing, gel electrophoresis, plasmid transformation and purification, polymerase chain reaction, Deoxyribonucleic Acid (DNA) structure, recombinant techniques, quantitation, sequencing, and microarray.
16 May
Improved nearest centroid classier with
The null LDA technique is used for dimensionality reduction and the classier is applied on reduced dimensional feature space. The SD-NCC is compared with other classiers on several DNA microarray gene expression data and encouraging results have been noted. ... A. Sharma and K.K. Paliwal (Signal Processing Lab, Grifth University, Brisbane, QLD-4111, Australia). E-mail: sharma_al@usp.ac.fj. References.
Algorithm for missing value estimation for dna microarray data
DNA microarrays are used as a tool for analyzing information in gene expression data over a broad range of biological applica-tions such as cancer classication [9], cancer prognosis [13] and identications of cell cycle-regulated genes of yeast [14]. During the laboratory process, some spots on the array may be missing due to various factors (for example, machine error.)
ACDSee 32 print job
Links to the page contain: Lokalization techniques in Lp spaces....
Lab 8 | DNA Structure
Lab 8. Extracting DNA from Your Cells. ... After completing this lab exercise you should be able to..... 1. Extract DNA from some of your cells 2. Learn about the structure, function and replication of DNA. Prelab Questions 1. Why is DNA so important in biology?
MACE: Lossless Compression and
Experimental results indicate that the MACE application offers a compelling alternative to currently available techniques in microarray image storage and analysis and can significantly ameliorate the critical challenges associated with storage, analysis, and exchange of primary (image-based) microarray data. ACKNOWLEDGEMENTS. We would like to thank Dr. Jonathan Pollack, of the Pollack Lab and Janos Demeter, the Microarray Curator, both of Stanford University for their valuable assistance in providing sample microarray images.
Laboratory Techniques
7 November
eCite - Saliva-Derived DNA Performs Well in Large-Scale...
Saliva-Derived DNA Performs Well in Large-Scale, High-Density Single-Nucleotide Polymorphism Microarray Studies...
30 November
Links to descriptions of chemistry lab techniques
Links to descriptions of chemistry lab techniques. ... Links to Descriptions of Chemistry Laboratory Techniques. Vacuum Filtration.
5 January
Lab 4: DNA Barcoding
Lab 4: DNA Barcoding. Objectives There are two major goals of this three-week lab. The first is to introduce you to the technology and methods of DNA sequence data applied to the specific problem of identifying the fish larvae sampled during the Plankton cruises. ... Unnecessary rough treatment breaks down the sample, reducing DNA quality and quantity. We are depending on your best laboratory technique to make these new discoveries.
Origins: Cold Spring Harbor Lab: The Genome... | Exploratorium
—Vivek Mittal, researcher in cancer genomics and DNA array technology at Cold Spring Harbor Laboratory (CHSL). "The primary goal is discovery, particularly in fundamental areas, and there is sufficient room made available for investigators to pursue their own interests. ... In this video, medical geneticist Eli Hatchwell and cancer researcher Vivek Mittal of the Genome Center at Cold Spring Harbor Laboratory show the process of creating a DNA microarray.
26 December
Free downloads | ANU Press
Links to the page contain: Mitochondrial DNA of Human Remains at Man Bac - ANU Press....
10 January
Doctor’s guide
Chromosome microarray in Australia: A guide for paediatricians. Journal of Paediatrics and Child Health 48 (2012) E59–E67. 1. Patient to undergo CMA testing, a genetic test which checks for DNA copy number variations, not including fragile X 2. Discussion of test process, limitations and counselling about variety of possible outcomes listed below 3. Blood sample collected (5-10ml in EDTA - Confirm sample requirements with local laboratory) 4. Possible laboratory findings include the following
Pitt Community College :: Academics :: Programs :: Arts And...
Upon completion, students should have an understanding of the theory, practice, and application of recombinant DNA techniques. There is a $11.25 lab fee for this course. ... Topics include cloning, sequencing and analysis of DNA samples, PCR/qPCR/RT-PCR, DNA typing (STR analysis), microarrays, and bioinformatics applications. Upon completion, students should be able to discuss and perform advanced genetic, biochemical, and bioinformatic procedures using reagents and equipment according to prescribed protocols.
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