Navigation Links
The Flexible matriXarray Chip System: A New Perspective,,,for Probe Optimization in Gene-Expression Profiling

In general, oligonucleotide microarrays are composed of a two- or three-dimensional solid surface where DNA, used as a capture molecule (probe), is attached in an orderly fashion. Each of the oligonucleotide probes on the microarray corresponds to a specific target gene, allowing the researcher to hybridize and detect multiple sequences in parallel. The synthesis principle of the oligonucleotides varies among different microarray platforms. Probe sequences can be synthesized ex situ and may then be robotically spotted onto the surface, or probe sequences can be synthesized in situ on the surface of the array.

The Virtual Flask Technology

CombiMatrix Corporation has developed a proprietary electrochemical on-chip synthesis principle. The oligonucleotide probes are synthesized in situ on a special reaction matrix above the semiconductor-based supportive material. A special buffer system allows the generation of so-called virtual flasks in which the oligonucleotide synthesis takes place. Each feature (electrode) on the array is individually addressable and thus allows the fast production of a customized chip (Figure 1).

The matriXarray Chip System from Roche Applied Science is built upon this virtual flask technology (Figure 2). Arrays are ordered online, produced in a quality-controlled environment, and delivered within a bar codelabeled protective flow cell. The HybReader Instrument, a walk-away device for array hybridization and imaging; the corresponding buffer sets; and a software suite for image processing, data extraction, and data mining, complete the integrated matriXarray Chip System.

Probe Optimization Is Crucial

The importance of the flexible production of customized arrays becomes obvious when different probes that detect the same gene are analyzed. Probe design software solutions are not yet able to provide probes with identical thermodynamic behavior. Furthermore, the in silico check for probe specificity is largely related to the transcriptome analyzed, as well as to the amount of sequence information available. Even for the human genome, this information is far from being complete. Currently, microarray vendors are addressing this problem with two different approaches. In the first approach, one probe per gene is offered with in silico and sometimes experimental validation. In the other approach, different probes per gene are used together with platformspecific algorithms to calculate the result. In conclusion, the optimization of probes used in array experiments is of major importance, especially when questions concerning genome-wide screening of gene-expression profiles must be answered.

New Concept for Probe Optimization

Roche Applied Science has developed a new concept for probe optimization using the matriXarray Chip System. The systematic approach analyzes probe profiles and is based on the assumption that specific probes show similar signal-intensity patterns in different samples (e.g., tissues). Preliminary experiments in three different rat tissues demonstrate the feasibility of this approach: a total of 57 different genes are included in the analysis (15 specific for kidney, 1 specific for kidney and liver, 18 specific for liver, and 23 specific for brain) together with 11 housekeeping genes. The chips were hybridized in duplicate. The mean average signal intensity after local background correction and normalization between the tissues via housekeeping genes was calculated. To demonstrate the approach, the resulting probe profiles of one gene for each tissue are displayed in Figure 3.

The comparison of probe profiles reveals the similar behavior of some probes, while others show distinct differences. For the brain-specific gene (GenBank acc. no. AB049056), all five probes show the same tendency; however, probes 3 and 4 display the most preferred pattern due to their high degree of profile similarity and specificity for the brain tissue. Representing the liver-specific gene (GenBank acc. no. J02585), probes 2, 5, and 6 display similar attributes; however, especially probes 4 and 7 show a more distinct pattern (a high signal in brain and/or kidney and a lower signal in liver compared to the other probes), indicating a dysfunction of these two probes. For the kidney- specific gene (GenBank acc. no. AF062389), probes 2, 5, 6, and 7 seem to be specific, while probes 1, 3, and 4 show aberrations in their intensity pattern.

In an ongoing study, the expression levels of 130 genes in 5 different human tissues are analyzed. The goal of this study is to establish an automated workflow for probe selection.

Fast and Convenient Iteration of Chip Layout

In conclusion, the data shown here demonstrate the impact of experimental probe validation in gene-expression profiling experiments. Based on the high flexibility in the production of customized chips, the matriXarray Chip System is the first platform that allows a fast and convenient iteration of chip layouts. Since probe optimization is crucial for all microarray applications, future work will extend this approach to applications outside of expression profiling, such as mutation detection and the analysis of splice variants.


'"/>

Source:


Page: All 1 2 3 4

Related biology technology :

1. The LightCycler is the only System for Quantitative PCR that is as Flexible as You are!
2. TripleMaster PCR System: Direct Comparison with Competitors
3. New Microarray Labeling Kit for Preparing cDNA Probes
4. QuantiTect Probe PCR Kit
5. RNase Protection Assay (RPA) Using DIG-Labeled RNA Probes
6. Detection of mRNAs on Cryosections of the Cardiovascular System Using DIG-Labeled RNA Probes
7. Prepare siRNA and miRNA Probes in Just 1 Hour
8. Rapidly Prepare Probes and Markers for Small RNA Analysis
9. New statistical algorithms for Monitoring Gene Expression on GeneChip® Probe Arrays
10. Two-dimensional Optimization of a Semi-nested PCR for Detecting Listeria monocytogenes
11. PCR Optimization
Post Your Comments:
(Date:8/28/2014)... August 28, 2014 Supplementing their ... a promotion for Eppendorf Safe Lock Centrifuge ... purchase the highest quality tubes at an affordable ... for customers doing chemical, medical, pharmaceutical, and life ... are not regularly able to afford Eppendorf products. ...
(Date:8/27/2014)... -- Rhythm, a biopharmaceutical company developing peptide therapeutics that ... metabolic disorders, announced today that it has filed a ... and Exchange Commission (SEC) relating to the proposed initial ... number of shares to be offered and the price ... Citigroup and Cowen and Company will act ...
(Date:8/27/2014)... is how plants survive impact by the huge ... while using this energy for photosynthesis. The hypothesis ... blades quickly dissipate the energy throughout the entire ... DTU Physics have now managed to successfully ,film, ... contain light-absorbing proteins which play a role in ...
(Date:8/27/2014)... 2014  Lisa Kulik saw fireworks for the first ... thanks to a groundbreaking retinal implant co-invented by ... at the University of Southern California (USC) Eye Institute. ... Ariz. resident who has retinitis pigmentosa, a ... On June 2, she became the first person west ...
Breaking Biology Technology:Eppendorf Safe Lock Centrifuge Tube Promotion Now Available at Major Pipette Distributor Pipette.com 2Eppendorf Safe Lock Centrifuge Tube Promotion Now Available at Major Pipette Distributor Pipette.com 3Rhythm Files Registration Statement for Proposed Initial Public Offering 2DTU researchers film protein quake for the first time 2USC Eye Institute ophthalmologists implant first FDA-approved Argus II retinal prosthesis in western United States 2USC Eye Institute ophthalmologists implant first FDA-approved Argus II retinal prosthesis in western United States 3USC Eye Institute ophthalmologists implant first FDA-approved Argus II retinal prosthesis in western United States 4USC Eye Institute ophthalmologists implant first FDA-approved Argus II retinal prosthesis in western United States 5
... 7 Abbott (NYSE: ABT ),will present ... on Tuesday, March 18, 2008. Thomas C. Freyman, ... make a formal,presentation on the company at 8:30 ... of the presentation will be accessible through,Abbott,s Investor ...
... On Thursday, March 13, 2008,at 8:30 a.m. ... Therapeutics, Inc.,s (CTI) (Nasdaq: CTIC ; MTAX) ... discuss the company,s 2007 fourth,quarter achievements and year-end ... Thursday, March 13 8:30 a.m. Eastern/1:30 p.m. ...
... team of researchers from the departments of macromolecular science ... of Engineering and the Louis Stokes Cleveland Department of ... a new type of polymer that displays chemoresponsive mechanic ... to soft plastic and vice versa in seconds when ...
Cached Biology Technology:Researchers engineer new polymers to change their stiffness and strength when exposed to liquids 2Researchers engineer new polymers to change their stiffness and strength when exposed to liquids 3
(Date:8/27/2014)... listen carefully to someone, the first thing we do ... stop moving altogether. This strategy helps us hear better ... , This interplay between movement and hearing also has ... has long suggested that the brain,s motor cortex, which ... rise to our conscious perception of sound. , A ...
(Date:8/27/2014)... beasts. But every creature is a baby once. , ... of 24 very young dinosaurs and one older individual ... a caretaker, according to a new study by University ... Peter Dodson led the work, collaborating with researchers from ... is held. Hedrick is a doctoral student in the ...
(Date:8/27/2014)... evidence puts into doubt the long-standing belief that a ... brain plays a central role in depression. In ... that mice lacking the ability to make serotonin in ... conventional wisdom) did not show depression-like symptoms. , ... VA Medical Center and Wayne State University School of ...
Breaking Biology News(10 mins):Stop and listen: Study shows how movement affects hearing 2Stop and listen: Study shows how movement affects hearing 3Penn paleontologists describe a possible dinosaur nest and young 'babysitter' 2Penn paleontologists describe a possible dinosaur nest and young 'babysitter' 3New study throws into question long-held belief about depression 2
... States are markedly underestimating the changes needed to mitigate ... change because they work in ,silos, according to pioneering ... Manchester, discovered that the lack of communication between government ... differences over who is responsible for what. He ...
... fibrillation is a cardiac arrhythmia a chronic irregularity ... people in Germany. Although the condition is not acutely ... serious illnesses, such as cardiac insufficiency, stroke and dementia. ... studies, an international team of researchers, led by LMU ...
... as the "world,s aquarium," the marine ecosystems of the ... methods are depleting the sea,s habitats, creating areas that ... story "Threatened Gulf" . But, as Octavio ... Diego will describe during a presentation at the 2010 ...
Cached Biology News:Governments 'misjudging' scale of CO2 emissions 2When the heart gets out of step 2When the heart gets out of step 3Damage to threatened Gulf of California habitats can be reversed 2
...
...
... Solid phase reagent ... purification; Easy & unique ... Compatible with detergents and ... & recover non-envelop viruses ...
Synaptic Vesicle I Sampler Kit 10g each...
Biology Products: