Name: technical demonstration of whole genome array comparative genomic hybridization
Uploaded: 2008-08-05T18:06:00.000+00:00
Duration: 16 min 37 s
Description: Watch this Scientific Journal Video about Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization at JoVE.com

Wir wünschen den Mitgliedern des Wan Lam Lab BAC-Array-Team vor allem Miwa Suzuki und Bryan Chi für die Vorbereitung dieses Artikels danken. Diese Arbeit wurde durch Mittel aus Canadian Institutes for Health Research, Genome Canada / Genome British Columbia, und NIH / NIDCR gewähren RO1 DE15965-01 unterstützt.

Sondenmarkierung Hinweis: Begrenzung der Exposition Cye Farbstoffe, um Licht zu jeder Zeit (dies kann durch die Arbeit in einem abgedunkelten Raum oder durch Abschirmung der Rohre mit einer Abdeckung wie Aluminiumfolie erreicht werden) <ol><li> Kombinieren Sie: (Setup 1 Reaktionsgefäß als Referenz und 1 Reaktionsrohr Probe) <ul><li> DNA (25-400 ng) </li><li> 5 ul 5X random Primer (Endkonzentration: 5X Promega Klenow-Puffer und 7 ug / ul random Octamere) </li><li> Verdünnen auf 17,0 ul Gesamtvolumen mit destilliertem H 2 O </li></ul></li><li> Kochen für 10 Minuten bei 100 ° C. Sofort auf Eis für 1 Minute. </li><li> Add 4 ul 10x dNTP-Mix (2 mM dATP, dGTP, dTTP, dCTP 1,2 mm). </li><li> Add CyeDyes: <ul><li> Add 2 ul (2 nmol) von Cy-3 markiertem dCTP zu Proben-DNA </li><li> Add 2 ul (2 nmol) von Cy-5 markierten dCTP zu Referenz-DNA (zB Novagen humanen genomischen DNA) </li></ul></li><li> Add 2,5 ul Klenow (9 U / ul, Promega) und mischen. </li><li> Bei 37 ° C über Nacht * (~ 18 Stunden). * Die Hybridisierung über Nacht kann zwischen 14 bis 24 Stunden ohne Beeinträchtigung der Labelling-Verfahren in ein Labor Zeitplan passen eingestellt werden. </li></ol> Probenaufbereitung (Combined Sonde clean-up und Vorbereitung für die Hybridisierung) <ol><li> Mit einem Microcon YM-30 Spalte: <ul><li> 100 l Cot-1 DNA (1μg/μL) in die Spalte. Berühren Sie nicht Membran mit Pipettenspitze. </li><li> Pool der Reaktionen (Referenz und Probe) und fügen Sie in die Spalte. </li><li> Legen Spalte in sofern Rohr und Spin bei 13000 g für 10 Minuten. </li><li> Geben Sie 200 ul destilliertem H 2 0 auf die Membran und wiederholen Spin zu waschen. </li><li> Discard Tube und füge 45 ul Hybridisierungslösung: (Roche DIG Easy) </li></ul> Optional: add 5μL geschert Heringssperma DNA (10μg/μL Einheit, Promega) <ul><li> Invert Microcon, Platz in einer neuen Bezeichnung Rohr und drehen sich mit 3000 g für 3 Minuten. </li></ul></li></ol> BERECHNUNG Eingemeindungen <ol><li> Entfernen 1,5 ul und messen Fluorophor Einbau mit NanoDrop Spektralphotometer. Mit Ihrem Hybridisierungspuffer wie eine leere (DIG Easy) folgen Sie den Anweisungen auf dem Bildschirm. (Sie können die Probe aus dem Sockel zu erholen, falls erforderlich, nach der Messung.) (Hinweis:. Incorporations unter 3,0 pmol / ul in einem der Kanäle zeigten unterschiedliche Ergebnisse) </li><li> Denaturieren bei 85 ° C für 10 Minuten. </li><li> Legen Sonde bei 45 ° C für 30 Minuten bis 1 Stunde (erlaubt Cot-1 DNA Glühen.) </li></ol> ARRAY HYBRIDIZATION <ol><li> Platz 44 ul Probe-Lösung auf das Deckglas (22 mm x 60 mm) (Fisher Scientific). Falls vorhanden, legen Sie das Deckglas auf einem Objektträger wärmer oder Heizblock auf 45 vorgewärmten ° C auf Temperatur zu halten. </li><li> Richten Sie gleiten über Deckglas und Probe-Lösung, untere Kante der Folie ermöglicht den Kontakt mit der Hybridisierungslösung. Weiter zu senken, bis das Deckglas auf dem Objektträger mit der Oberflächenspannung verbunden ist. Invert gleiten. </li><li> Legen Sie die Folie in Hybridisierung Kassette (Telechem), vorgewärmt auf 45 ° C, und fügen Sie 10 l Wasser in die untere Nut (gegen Feuchtigkeit während der Hybridisierung Steuerung). </li><li> Seal Kassette und inkubieren 36 bis 40 Stunden bei 45 ° C. </li></ol> ARRAY WASCHEN Hinweis: Alle Waschlösungen werden bei pH 7,0 Das Entfernen der Folie aus der Hybridisierung Kassette ist kritisch. DIG Easy schnell kristallisiert bei Raumtemperatur. Der Schlitten sollte sofort eingetaucht werden und das Deckglas in der Waschlösung entfernt. <ol><li> Fügen Sie ca. 60 ml 0.1XSSC, 0,1% SDS (pH 7,0, 45 ° C) waschen Lösung für ein Coplin Glas vor dem Öffnen der Hybridisierung Kammer. </li><li> Offene Kammer, fügen Folie Lösung zu waschen und zu entfernen Deckglas (es sollte abrutschen). </li><li> Waschen Sie die Folie 3 mal in 0.1XSSC + 0,1% SDS bei 45 ° C für 1 Minute unter Rühren. </li><li> Spülen Sie die Folie 3 mal in frischem 0.1XSSC *. Es sollte kein Rest-Blasen aus dem SDS waschen sichtbar werden. * Die Folien können in der letzten Waschlösung bis zu seiner Zentrifuge und Scannen (~ 15 Minuten) bleiben. </li><li> Zentrifugieren Sie die Folie in einer 50 ml Falcon-Röhrchen bei 700 g für 3 Minuten. </li><li> Unmittelbar scannen die Dias (Signalintensitäten im Laufe der Zeit abnehmen.) </li></ol>

<ol>
	<li>Lockwood, W. W., Chari, R., Chi, B., Lam, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recent+advances+in+array+comparative+genomic+hybridization+technologies+and+their+applications+in+human+genetics.">Recent advances in array comparative genomic hybridization technologies and their applications in human genetics.</a> European Journal of Human Genetics. 14, 139-1x`48 (2006).</li><li>Ishkanian, A. S., Malloff, C. A., Watson, S. K., deLeeuw, R. J., Chi, B., Coe, B. P., Snijders, A., Albertson, D. G., Pinkel, D., Marra, M. A., Ling, V., MacAulay, C., Lam, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+tiling+resolution+DNA+microarray+with+complete+coverage+of+the+human+genome.">A tiling resolution DNA microarray with complete coverage of the human genome.</a> Nature Genetics. 36, 299-303 (2004).</li><li>Watson, S. K., DeLeeuw, R. J., Ishkanian, A. S., Malloff, C. A., Lam, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+for+high+throughput+validation+of+amplified+fragment+pools+of+BAC+DNA+for+constructing+high+resolution+CGH+arrays.">Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays.</a> BMC Genomics. 5, 6 (2004).</li><li>Watson, S. K., DeLeeuw, R. J., Horsman, D. E., Squire, J. A., Lam, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytogenetically+balanced+translocations+are+associated+with+focal+copy+number+alterations.">Cytogenetically balanced translocations are associated with focal copy number alterations.</a> Human Genetics. 120, 795-805 (2007).</li><li>Chi, B., DeLeeuw, R. J., Coe, B. P., MacAulay, C., Lam, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SeeGH+--+a+software+tool+for+visualization+of+whole+genome+array+comparative+genomic+hybridization+data.">SeeGH -- a software tool for visualization of whole genome array comparative genomic hybridization data.</a> BMC Bioinformatics. 5, 13 (2004).</li><li>Chi, B., DeLeeuw, R. J., Coe, B. P., Ng, R. T., MacAulay, C., Lam, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MD-SeeGH:+a+platform+for+integrative+analysis+of+multi-dimensional+genomic+data.">MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data.</a> BMC Bioinformatics. 9, 243 (2008).</li><li>Coe, B. P., Ylstra, B., Carvalho, B., Meijer, G. A., Macaulay, C., Lam, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resolving+the+resolution+of+array+CGH.">Resolving the resolution of array CGH.</a> Genomics. 89, 647-653 (2007).</li><li>Garnis, C., Coe, B. P., Lam, S. L., MacAulay, C., Lam, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-resolution+array+CGH+increases+heterogeneity+tolerance+in+the+analysis+of+clinical+samples.">High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples.</a> Genomics. 85, 790-793 (2005).</li></ol>

Schlechte Qualität DNA wird nicht eine gute Hybridisierung Profil. Es ist wichtig, dass die Probe zu gewährleisten und Referenz-DNA sind frei von Verunreinigungen wie Phenol, RNA, Salz, etc, die mit dem random prime Kennzeichnung Schritt vor Beginn einer Hybridisierung Experiment stören können. Zum Beispiel die Resuspension der DNA in Tris - EDTA (TE) anstelle von Wasser ist nicht so hohe Salzkonzentration empfohlen hemmen können die Kennzeichnung Reaktion. Wir empfehlen Testen DNA-Qualität mit dem Nanodrop Spektralphotometer, um sowo...

<table><tbody><tr><td>5X Klenow Buffer</td><td>Reagent</td><td>Promega Corp.</td><td></td><td></td></tr><tr><td>Random Octamers </td><td>Reagent</td><td>Alpha DNA</td><td></td><td></td></tr><tr><td>10X dNTP mix</td><td>Reagent</td><td>Promega Corp.</td><td></td><td>2mM dATP, dGTP, dTTP, 1.2mM dCTP</td></tr><tr><td>Cy-3 labeled dCTP</td><td>Reagent</td><td>GE Healthcare</td><td></td><td></td></tr><tr><td>Cy-5 labeled dCTP</td><td>Reagent</td><td>GE Healthcare</td><td></td><td></td></tr><tr><td>Human Genomic DNA Reference</td><td>Reagent</td><td>Novagen, EMD Millipore</td><td></td><td>Example of a possible reference</td></tr><tr><td>Klenow</td><td>Reagent</td><td>Promega Corp.</td><td></td><td></td></tr><tr><td>YM-30 Column</td><td>Reagent</td><td>EMD Millipore</td><td></td><td></td></tr><tr><td>Cot-1 DNA</td><td>Reagent</td><td>Invitrogen</td><td></td><td></td></tr><tr><td>DIG Easy</td><td>Reagent</td><td>Roche Group</td><td></td><td></td></tr><tr><td>Sheared Herring Sperm DNA</td><td>Reagent</td><td>Promega Corp.</td><td></td><td></td></tr><tr><td>Coverslip</td><td>Reagent</td><td>Fisher Scientific</td><td></td><td>22mm x 60mm</td></tr><tr><td>Hybridization Cassette</td><td>Tool</td><td>Telechem</td><td></td><td></td></tr></tbody></table>

technical demonstration of whole genome array comparative genomic hybridization

Array komparative genomische Hybridisierung (Array-CGH) ist eine Methode zum Nachweis von Gewinnen und Verlusten von DNA-Segmenten oder Gen-Dosierung in das Genom 1. Jüngste Fortschritte in dieser Technologie sind mit hochauflösenden Vergleich ganzer Genome für die Identifizierung genetischer Veränderungen bei Krebs und anderen genetischen Erkrankungen 2 aktiviert. Die Sub-Megabase Resolution Tiling-set array (oder SMRT)-Array besteht aus einer Reihe von rund 30.000 überlappenden bakterielle künstliche Chromosom (BAC) Klone, die das menschliche Genom in ~ 100 Kilobasenpaar (kb) Segmente 2 span zusammen. Diese BAC-Ziele werden individuell hergestellt und entdeckte in zweifacher Ausfertigung auf einem einzigen Objektträger 2-4. Array-CGH ist auf dem Prinzip der kompetitiven Hybridisierung. Proben-und Referenz-DNA werden differentiell mit Cyanin-3 bezeichnet und Cyanine-5 Fluoreszenzfarbstoffe, und das Array co-hybridisiert. Nach einer Inkubationszeit die ungebundenen Proben werden von der Folie gewaschen und das Array abgebildet. Eine frei verfügbare kundenspezifische Software-Paket namens SeeGH (www.flintbox.ca) wird verwendet, um die große Menge an Daten gesammelt Prozess - einem einzigen Experiment erzeugt 53.892 Datenpunkte. SeeGH visualisiert die log2 Signalintensität Verhältnis zwischen den 2 Proben an jedem BAC Ziel, die vertikal mit chromosomalen Position 5,6 ausgerichtet ist. Der SMRT Array erkennt Änderungen so klein wie 50 kb in Größe 7. Der SMRT Array erkennt eine Vielzahl von DNA Umlagerung Veranstaltungen, darunter DNA Gewinne, Verluste, Amplifikationen und homozygote Deletionen. Ein einzigartiger Vorteil der SMRT Array ist, dass man DNA aus Formalin-fixierten Paraffin eingebetteten Proben isoliert zu verwenden. In Verbindung mit dem niedrigen Eingang Anforderungen der unverstärkten DNA (25-100 ng) kombiniert dies ermöglicht Profilierung der wertvollen Proben, wie sie durch Mikrodissektion 7,8 produziert. Dies ist auf die Größe der einzelnen BAC-Hybridisierung Ziel, dass die Bindung von ausreichend markierten Proben, um Signale für den Nachweis produzieren können zugeschrieben. Ein weiterer Vorteil dieser Plattform ist die Toleranz des Gewebes Heterogenität, der Bedarf an langwierige Gewebe Mikrodissektion 8. Dieses Video-Protokoll ist ein Schritt-für-Schritt-Anleitung von der Kennzeichnung der eingesetzten DNA bis hin zur Übernahme des gesamten Genoms Fliesen Weg SMRT Array Signal.

Watch this Scientific Journal Video about Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization at JoVE.com

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Dieses Video ist eine technische Demonstration der Hybridisierung Protokoll für gesamte Genom Fliesen Weg Array-CGH, ​​die das gesamte menschliche Genom mit nur 25-100 ng DNA, die aus einer Vielzahl von Quellen, einschließlich Archivierung Formalin fixiert Material isoliert werden können Scans.

Technische Demonstration von Whole Genome Array Comparative Genomic Hybridization

Array comparative genomic hybridization (array CGH) is a method for detecting gains and losses of DNA segments or gene dosage in the genome 1.  Recent ...

technical-demonstration-whole-genome-array-comparative-genomic

Research

JoVE Journal

Biology

12.7K Aufrufe.  BC Cancer Research Centre. *The slides can remain in the 

Serie: Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to particular habitats and management practices. This article shows how certain terroir signatures can be detected in the berry metabolome and transcriptome of the grapevine cultivar Corvina using multivariate statistical analysis. The method first requires an appropriate sampling plan. In this case study, a specific clone of the Corvina cultivar was selected to minimize genetic differences, and samples were collected from seven vineyards representing three different macro-zones during three different growing seasons. An untargeted LC-MS metabolomics approach is recommended due to its high sensitivity, accompanied by efficient data processing using MZmine software and a metabolite identification strategy based on fragmentation tree analysis. Comprehensive transcriptome analysis can be achieved using microarrays containing probes covering ~99% of all predicted grapevine genes, allowing the simultaneous analysis of all differentially expressed genes in the context of different terroirs. Finally, multivariate data analysis based on projection methods can be used to overcome the strong vintage-specific effect, allowing the metabolomics and transcriptomics data to be integrated and analyzed in detail to identify informative correlations.

This article describes the application of untargeted metabolomics, transcriptomics and multivariate statistical analysis to grape berry transcripts and metabolites in order to gain insight into the terroir concept, i.e., the impact of the environment on berry quality traits.

Das Terroir-Konzept Interpretiert durch Grape Berry Metabolomics und Transcriptomics

Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to ...

Forschung

Genetik

An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants

Mutants are invaluable genetic resources for gene function studies. To generate mutant collections, three types of mutagens can be utilized, including biological such as T-DNA or transposon, chemical such as ethyl methanesulfonate (EMS), or physical such as ionization radiation. The type of mutation observed varies depending on the mutagen used. For ionization radiation induced mutants, mutations include deletion, duplication, or rearrangement. While T-DNA or transposon-based mutagenesis is limited to species that are susceptible to transformation, chemical or physical mutagenesis can be applied to a broad range of species. However, the characterization of mutations derived from chemical or physical mutagenesis traditionally relies on a map-based cloning approach, which is labor intensive and time consuming. Here, we show that a high-density genome array-based comparative genomic hybridization (aCGH) platform can be applied to efficiently detect and characterize copy number variations (CNVs) in mutants derived from fast neutron bombardment (FNB) mutagenesis in Medicago truncatula, a legume species. Whole genome sequence analysis shows that there are more than 50,000 genes or gene models in M. truncatula. At present, FNB-induced mutants in M. truncatula are derived from more than 150,000 M1 lines, representing invaluable genetic resources for functional studies of genes in the genome. The aCGH platform described here is an efficient tool for characterizing FNB-induced mutants in M. truncatula.

An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants

This protocol provides experimental steps and information about reagents, equipment, and analysis tools for researchers who are interested in carrying out whole genome array-based comparative genomic hybridization (CGH) analysis of copy number variations in plants.

Eine Array-basierte Comparative genomische Hybridisierung Plattform für effiziente Erkennung der Kopie Zahl Variationen in schnellen Neutronen induziert Medicago Truncatula Mutanten

Mutants are invaluable genetic resources for gene function studies. To generate mutant collections, three types of mutagens can be utilized, including ...

High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries

Photolithography is a powerful technique for the synthesis of DNA oligonucleotides on glass slides, as it combines the efficiency of phosphoramidite coupling reactions with the precision and density of UV light reflected from micrometer-sized mirrors. Photolithography yields microarrays that can accommodate from hundreds of thousands up to several million different DNA sequences, 100-nt or longer, in only a few hours. With this very large sequence space, microarrays are ideal platforms for exploring the mechanisms of nucleic acid&#183;ligand interactions, which are particularly relevant in the case of RNA. We recently reported on the preparation of a new set of RNA phosphoramidites compatible with in situ photolithography and which were subsequently used to grow RNA oligonucleotides, homopolymers as well as mixed-base sequences. Here, we illustrate in detail the process of RNA microarray fabrication, from the experimental design, to instrumental setup, array synthesis, deprotection and final hybridization assay using a template 25mer sequence containing all four bases as an example. In parallel, we go beyond hybridization-based experiments and exploit microarray photolithography as an inexpensive gateway to complex nucleic acid libraries. To do so, high-density DNA microarrays are fabricated on a base-sensitive monomer that allows the DNA to be conveniently cleaved and retrieved after synthesis and deprotection. The fabrication protocol is optimized so as to limit the number of synthetic errors and to that effect, a layer of &#946;-carotene solution is introduced to absorb UV photons that may otherwise reflect back onto the synthesis substrates. We describe in a step-by-step manner the complete process of library preparation, from design to cleavage and quantification.

In this article, we present and discuss new developments in the synthesis and applications of nucleic acid microarrays fabricated in situ. Specifically, we show how the protocols for DNA synthesis can be extended to RNA and how microarrays can be used to create retrievable nucleic acid libraries.

High-Density DNA und RNA Mikroarrays - Photolithographische Synthese, Hybridisierung und Vorbereitung von großen Nukleinsäurebibliotheken

Photolithography is a powerful technique for the synthesis of DNA oligonucleotides on glass slides, as it combines the efficiency of phosphoramidite ...

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform

Gene microarray technology permits quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. Gene microarray technology is used in numerous biological disciplines in a variety of applications including global gene expression analysis in relation to developmental stage, to a disease state, and in toxic responses. Herein, we include a demonstration of global gene expression analysis using a comprehensive zebrafish-specific oligonucleotide microarray platform. The zebrafish expression microarray platform contains 385,000 probes, 60 base pairs in length, interrogating 37,157 targets with up to 12 probes per target. For this platform, all cDNA and genomic information available for the zebrafish was collected from various genomic databases including Ensembl (http://www.ensembl.org), VEGA (http://vega.sanger.ac.uk), UCSC (http://genome.ucsc.edu), and ZFIN (http://www.zfin.org). As a result this expression array provides complete coverage of the current zebrafish transcriptome. The zebrafish expression microarray was printed by Roche NimbleGen (Madison, WI). This technical demonstration includes the fluorescent labeling of a cDNA product, hybridization of the labeled cDNA product to the microarray platform, and array scanning for signal acquisition using the one color analysis strategy.  

Gene microarrays are powerful tools in gene expression profiling at a genome-wide level. This technology has application in a variety of biological disciplines including developmental biology and toxicology. In this video, we detail a protocol for global gene expression analysis using a comprehensive oligonucleotide microarray platform for the zebrafish.

Globale Genexpressionsanalyse Mit einem Zebrafisch Oligonukleotid-Microarray-Plattform

Gene microarray technology permits quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. Gene microarray ...

Biologie

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Sequencing RNAs that co-immunoprecipitate (co-IP) with RNA binding proteins has increased our understanding of splicing by demonstrating that binding location often influences function of a splicing factor.  However, as with any sampling strategy the chance of identifying an RNA bound to a splicing factor is proportional to its cellular abundance.  We have developed a novel in vitro approach for surveying binding specificity on otherwise transient pre-mRNA. This approach utilizes a specifically designed oligonucleotide pool that tiles across introns, exons, splice junctions, or other pre-mRNA.  The pool is subjected to some kind of molecular selection. Here, we demonstrate the method by separating the oligonucleotide into a bound and unbound fraction and utilize a two color array strategy to record the enrichment of each oligonucleotide in the bound fraction. The array data generates high-resolution maps with the ability to identify sequence-specific and structural determinates of ribonucleoprotein (RNP) binding on pre-mRNA.  A unique advantage to this method is its ability to avoid the sampling bias towards mRNA associated with current IP and SELEX techniques, as the pool is specifically designed and synthesized from pre-mRNA sequence. The flexibility of the oligonucleotide pool is another advantage since the experimenter chooses which regions to study and tile across, tailoring the pool to their individual needs.  Using this technique, one can assay the effects of polymorphisms or mutations on binding on a large scale or clone the library into a functional splicing reporter and identify oligonucleotides that are enriched in the included fraction.  This novel in vitro high-resolution mapping scheme provides a unique way to study RNP interactions with transient pre-mRNA species, whose low abundance makes them difficult to study with current in vivo techniques.  



A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Due to the transient nature of pre-mRNA, it can be difficult to isolate and study in vivo. Here, we present a novel in vitro approach to investigate RNA-protein interactions using a synthetic oligo pool that tiles across selected regions of pre-mRNA.

Eine schnelle High-Throughput-Verfahren zur Abbildung Ribonukleoproteine ​​(RNPs) on Human pre-mRNA

Sequencing RNAs that co-immunoprecipitate (co-IP) with RNA binding proteins has increased our understanding of splicing by demonstrating that binding ...

A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations

Birth defects that involve the cerebral cortex &#8212; also known as malformations of cortical development (MCD) &#8212; are important causes of intellectual disability and account for 20-40% of drug-resistant epilepsy in childhood. High-resolution brain imaging has facilitated in vivo identification of a large group of MCD phenotypes. Despite the advances in brain imaging, genomic analysis and generation of animal models, a straightforward workflow to systematically prioritize candidate genes and to test functional effects of putative mutations is missing. To overcome this problem, an experimental strategy enabling the identification of novel causative genes for MCD was developed and validated. This strategy is based on identifying candidate genomic regions or genes via array-CGH or whole-exome sequencing and characterizing the effects of their inactivation or of overexpression of specific mutations in developing rodent brains via in utero electroporation. This approach led to the identification of the C6orf70 gene, encoding for a putative vesicular protein, to the pathogenesis of periventricular nodular heterotopia, a MCD caused by defective neuronal migration.

A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations

Periventricular nodular heterotopia (PNH) is the most common form of malformation of cortical development (MCD) in adulthood but its genetic basis remains unknown in most sporadic cases. We have recently developed a strategy to identify novel candidate genes for MCDs and to directly confirm their causative role in vivo.

Eine neuartige Strategie verbindet Array-CGH, ganze Exome Sequenzierung und In Utero Elektroporation bei Nagetieren verursachenden Gene für Hirnfehlbildungen identifizieren

Birth defects that involve the cerebral cortex &#8212; also known as malformations of cortical development (MCD) &#8212; are important causes of ...

Neurowissenschaften

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Microarray expression profiling of the nervous system provides a powerful approach to identifying gene activities in different stages of development, different physiological or pathological states, response to therapy, and, in general, any condition that is being experimentally tested1. Expression profiling of neural tissues requires isolation of high quality RNA, amplification of the isolated RNA and hybridization to DNA microarrays. In this article we describe protocols for reproducible microarray experiments from brain tumor tissue2. We will start by performing a quality control analysis of isolated RNA samples with Agilent's 2100 Bioanalyzer "lab-on-a-chip" technology. High quality RNA samples are critical for the success of any microarray experiment, and the 2100 Bioanalyzer provides a quick, quantitative measurement of the sample quality. RNA samples are then amplified and labeled by performing reverse transcription to obtain cDNA, followed by in vitro transcription in the presence of labeled nucleotides to produce labeled cRNA. By using a dual-color labeling kit, we will label our experimental sample with Cy3 and a reference sample with Cy5. Both samples will then be combined and hybridized to Agilent's 4x44 K arrays. Dual-color arrays offer the advantage of a direct comparison between two RNA samples, thereby increasing the accuracy of the measurements, in particular for small changes in expression levels, because the two RNA samples are hybridized competitively to a single microarray. The arrays will be scanned at the two corresponding wavelengths, and the ratio of Cy3 to Cy5 signal for each feature will be used as a direct measurement of the relative abundance of the corresponding mRNA. This analysis identifies genes that are differentially expressed in response to the experimental conditions being tested.

We demonstrate the use of DNA microarrays for expression profiling of the nervous system. We describe RNA quality control, sample labeling, and array hybridization and scanning.

DNA Microarrays: Sample Quality Control, Array Hybridisierung und Scannen

Microarray expression profiling of the nervous system provides a powerful approach to identifying gene activities in different stages of development, ...

Competitive Genomic Screens of Barcoded Yeast Libraries

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily. The tempo of these advances is accelerating, promising greater depth and breadth. In light of these extraordinary advances, the need for fast, parallel methods to define gene function becomes ever more important. Collections of genome-wide deletion mutants in yeasts and E. coli have served as workhorses for functional characterization of gene function, but this approach is not scalable, current gene-deletion approaches require each of the thousands of genes that comprise a genome to be deleted and verified. Only after this work is complete can we pursue high-throughput phenotyping. Over the past decade, our laboratory has refined a portfolio of competitive, miniaturized, high-throughput genome-wide assays that can be performed in parallel. This parallelization is possible because of the inclusion of DNA 'tags', or 'barcodes,' into each mutant, with the barcode serving as a proxy for the mutation and one can measure the barcode abundance to assess mutant fitness. In this study, we seek to fill the gap between DNA sequence and barcoded mutant collections. To accomplish this we introduce a combined transposon disruption-barcoding approach that opens up parallel barcode assays to newly sequenced, but poorly characterized microbes. To illustrate this approach we present a new Candida albicans barcoded disruption collection and describe how both microarray-based and next generation sequencing-based platforms can be used to collect 10,000 - 1,000,000 gene-gene and drug-gene interactions in a single experiment.

We have developed comprehensive, unbiased genome-wide screens to understand gene-drug and gene-environment interactions. Methods for screening these mutant collections are presented.

Competitive Genomic Screens von Barcoded Hefe Bibliotheken

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily.  The tempo of these advances is ...

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of limited use in exploring bacterial two component regulatory systems with uncharacterized activation conditions. Such systems regulate transcription only when activated in the presence of unique signals. Since these signals are often unknown, the in vitro microarray based method described in this video article can be used to determine gene targets and binding sites for response regulators. This DNA-affinity-purified-chip method may be used for any purified regulator in any organism with a sequenced genome. The protocol involves allowing the purified tagged protein to bind to sheared genomic DNA and then affinity purifying the protein-bound DNA, followed by fluorescent labeling of the DNA and hybridization to a custom tiling array. Preceding steps that may be used to optimize the assay for specific regulators are also described. The peaks generated by the array data analysis are used to predict binding site motifs, which are then experimentally validated. The motif predictions can be further used to determine gene targets of orthologous response regulators in closely related species. We demonstrate the applicability of this method by determining the gene targets and binding site motifs and thus predicting the function for a sigma54-dependent response regulator DVU3023 in the environmental bacterium Desulfovibrio vulgaris Hildenborough.

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

This video article describes an in vitro microarray based method to determine the gene targets and binding sites for two component system response regulators.

DNA-Affinitäts-gereinigten Chip (DAP-Chip)-Methode, um Gene für bakterielle Ziele fest, Zwei-Komponenten-Systeme Regulatory

In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of ...

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Array CGH for the detection of genomic copy number variants has replaced G-banded karyotype analysis. This paper describes the technology and its application in a clinical diagnostic service laboratory. DNA extracted from a patient&#8217;s sample (blood, saliva or other tissue types) is labeled with a fluorochrome (either cyanine 5 or cyanine 3). A reference DNA sample is labeled with the opposite fluorochrome. There follows a cleanup step to remove unincorporated nucleotides before the labeled DNAs are mixed and resuspended in a hybridization buffer and applied to an array comprising ~60,000 oligonucleotide probes from loci across the genome, with high probe density in clinically important areas. Following hybridization, the arrays are washed, then scanned and the resulting images are analyzed to measure the red and green fluorescence for each probe. Software is used to assess the quality of each probe measurement, calculate the ratio of red to green fluorescence and detect potential copy number variants.

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Array CGH for the detection of genomic copy number variants has replaced G-banded karyotype analysis. This paper describes the technology and its application in a diagnostic service laboratory.

Technische Demonstration von Whole Genome Array Comparative Genomic Hybridization

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