Yenilik, British Columbia Bilgi Kalkınma Fonu ve Ulusal Bilimler ve Mühendislik Araştırma Konseyi (NSERC) Kanada Kanada Vakfı Biz, kıyı ve açık okyanus sularında düşük oksijen bölgelerde devam eden çalışmalar destek için teşekkür etmek istiyorum. MT ve SL Mikrobiyal Çeşitlilik ve Evrim (CMDE) TULA vakıf tarafından finanse edilen Merkezi burs tarafından desteklenmiştir. MT de Deutsche Forschungsgemeinschaft (DFG) burs desteği aldı.

<ol>
	<li>Zaikova, E., Hawley, A., Walsh, D. A., Hallam, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Seawater+sampling+and.">Seawater sampling and.</a> J Vis Exp. , (2009).</li><li>Walsh, D. A., Zaikova, E., Hallam, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large+volume+(20L+)+filtration+of+coastal+seawater+samples.">Large volume (20L+) filtration of coastal seawater samples.</a> J Vis Exp. 28, (2009).</li><li>Wright, J. J., Lee, S., Zaikova, E., Walsh, D. A., Hallam, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+Extraction+from+0.22+&#956;M+Sterivex+Filters+and+Cesium+Chloride+Density+Gradient+Centrifugation.">DNA Extraction from 0.22 &#956;M Sterivex Filters and Cesium Chloride Density Gradient Centrifugation.</a> J Vis Exp. 31, 10-3791 (2009).</li><li>Stein, J. L., Marsh, T. L., Wu, K. Y., Shizuya, H., DeLong, E. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+uncultivated+prokaryotes:+isolation+and+analysis+of+a+40-kilobase-pair+genome+fragment+from+a+planktonic+marine+archaeon.">Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon.</a> J. Bacteriol. 178, 591-599 (1996).</li><li>B&#233;j&#224;, O., Suzuki, O., Koonin, M. T., Aravind, E. V., Hadd, L., Nguyen, L. P. A., Villacorta, R., Amjadi, M., Garrigues, C., Jovanovich, S. B., Feldman, R. A., DeLong, E. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Construction+and+analysis+of+bacterial+artificial+chromosome+libraries+from+a+marine+microbial+assemblage.">Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.</a> Environ. Microbiol. 2, 516-529 (2000).</li><li>DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallam, S. J., Frigaard, N. -. U., Martinez, A., Sullivan, M. B., Edwards, R., Brito, B. R., Chisholm, S. W., Karl, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Community+genomics+among+stratified+microbial+assemblages+in+the+Ocean's+interior.">Community genomics among stratified microbial assemblages in the Ocean's interior.</a> Science. 311, 496-503 (2006).</li><li>Hallam, S. J., Putnam, N., Preston, C. M., Detter, J. C., Rokhsar, D., Richardson, P. M., DeLong, E. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reverse+methanogenesis:+testing+the+hypothesis+with+environmental+genomics.">Reverse methanogenesis: testing the hypothesis with environmental genomics.</a> Science. 305, 1457-1462 (2004).</li></ol>

Bir prosedür nasıl bir kıyı su numunesi elde edilen genomik DNA ile büyük bir takın fosmid kütüphane oluşturmak için en verimli şekilde açıklanmıştır. Up-stream genomik DNA ekstraksiyonu ayrı bir protokol [3] açıklanmıştır. Fosmid-kütüphane üretim çok adımlı bir süreç, planı dört sunulan adımları da dahil olmak üzere tüm prosedürü için en az 2-3 hafta süre. Genomik DNA ekstraksiyonu, en önemli adım ve tüm aşağı akım adımları çıkarılan geno...

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		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
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<tr>
<td>Step II</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>CopyControl&trade; Fosmid Library Production Kit</td>
<td>&nbsp;</td>
<td>EPICENTRE</td>
<td>CCFOS110</td>
<td>sufficient to generate 9-10 fosmid libraries</td>
</tr>
<tr>
<td>SeaPlaque Agarose</td>
<td>&nbsp;</td>
<td>Cambrex</td>
<td>50100</td>
<td>&nbsp;</td>
<tr>
<td>stirring hot plate</td>
<td>&nbsp;</td>
<td>Corning</td>
<td>PC-420D</td>
<td>&nbsp;</td>
<tr>
<td>1.0X TAE running buffer</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>CHEF Mapper XA pulsed field electrophoresis system including cooling module and variable speed pump</td>
<td>&nbsp;</td>
<td>Bio-Rad</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>&lambda; DNA-HindIII Digest</td>
<td>&nbsp;</td>
<td>NEB</td>
<td>N3012S</td>
<td>&nbsp;</td>
<tr>
<td>MidRange I PFG Marker</td>
<td>&nbsp;</td>
<td>NEB</td>
<td>N3551S</td>
<td>&nbsp;</td>
<tr>
<td>10,000X SYBR Gold</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>S11494</td>
<td>&nbsp;</td>
<tr>
<td>microwavable plastic wrap</td>
<td>&nbsp;</td>
<td>Saran premium wrap</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Safe Imager transilluminator</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>S37102</td>
<td>&nbsp;</td>
<tr>
<td>GELase Agarose Gel-Digesting Preparation</td>
<td>&nbsp;</td>
<td>EPICENTRE</td>
<td>G09100</td>
<td>&nbsp;</td>
<tr>
<td>scalpel</td>
<td>&nbsp;</td>
<td>Fisher Scientific</td>
<td>08-927-5D</td>
<td>&nbsp;</td>
<tr>
<td>Amicon Ultra-4 Centrifugal Filter Unit with Ultracel-10 membrane</td>
<td>&nbsp;</td>
<td>Millipore</td>
<td>UFC801024</td>
<td>&nbsp;</td>
<tr>
<td>Microcon YM-30 Centrifugal Filter Unit </td>
<td>&nbsp;</td>
<td>Millipore</td>
<td>42410</td>
<td>&nbsp;</td>
<tr>
<td>nuclease free water</td>
<td>&nbsp;</td>
<td>Ambion</td>
<td>AM9932</td>
<td>&nbsp;</td>
<tr>
<td>Quant-iT PicoGreen dsDNA Assay Kit *2000 assays*#</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>P7589</td>
<td>&nbsp;</td>
<tr>
<td>digital dry block heater</td>
<td>&nbsp;</td>
<td>VWR</td>
<td>12621-088</td>
<td>&nbsp;</td>
<tr>
<td>water bath</td>
<td>&nbsp;</td>
<td>VWR</td>
<td>14231-854</td>
<td>&nbsp;</td>
<tr>
<td>centrifuge</td>
<td>&nbsp;</td>
<td>Beckman Coulter</td>
<td>Avanti J-E</td>
<td>&nbsp;</td>
<tr>
<td>centrifuge rotor</td>
<td>&nbsp;</td>
<td>Beckman Coulter</td>
<td>JA 5.3</td>
<td>&nbsp;</td>
<tr>
<td>table top centrifuge</td>
<td>&nbsp;</td>
<td>Eppendorf</td>
<td>5415D</td>
<td>&nbsp;</td>
<tr>
<td>microcentrifuge tubes, 1.7 mL, clear</td>
<td>&nbsp;</td>
<td>Axygen</td>
<td>MCT-175-C</td>
<td>&nbsp;</td>
<tr>
<td>15 mL centrifuge tubes </td>
<td>&nbsp;</td>
<td>Fisher-Corning</td>
<td>430052</td>
<td>&nbsp;</td>
<tr>
<td>Step III</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>LB broth</td>
<td>&nbsp;</td>
<td>Fisher Scientific</td>
<td>BP 1426-2</td>
<td>&nbsp;</td>
<tr>
<td>MgSO4</td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>M2643</td>
<td>&nbsp;</td>
<tr>
<td>phage dilution buffer</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>10 mM Tris-HCl [pH 8.3], 100 mM NaCl, 10 mM MgCl2</td>
</tr>
<tr>
<td>cryogenic vials</td>
<td>&nbsp;</td>
<td>Fisher-Corning</td>
<td>430488</td>
<td>&nbsp;</td>
<tr>
<td>Step IV</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>96 well plate with lid</td>
<td>&nbsp;</td>
<td>Fisher-Corning</td>
<td>CS003370(3370)</td>
<td>&nbsp;</td>
<tr>
<td>384 well plate with lid</td>
<td>&nbsp;</td>
<td>Fisher-Corning</td>
<td>07201157(3680)</td>
<td>&nbsp;</td>
<tr>
<td>Petri dishes 100 O.D. x 15mm H</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>08-757-12</td>
<td>&nbsp;</td>
<tr>
<td>Petri dishes 150 Dia. x 15mmH</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>08-757-14</td>
<td>&nbsp;</td>
<tr>
<td>BD Falcon BioDish XL 245 X 245 mm</td>
<td>&nbsp;</td>
<td>VWR</td>
<td>CABD351040</td>
<td>&nbsp;</td>
<tr>
<td>glycerol</td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>G5516</td>
<td>&nbsp;</td>
<tr>
<td>chloramphenicol</td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>C0378</td>
<td>&nbsp;</td>
<tr>
<td>LB broth</td>
<td>&nbsp;</td>
<td>Fisher Scientific</td>
<td>BP 1426-2</td>
<td>&nbsp;</td>
<tr>
<td>Difco Agar</td>
<td>&nbsp;</td>
<td>BD</td>
<td>214530</td>
<td>&nbsp;</td>
<tr>
<td>glass beads</td>
<td>&nbsp;</td>
<td>Fisher Scientific</td>
<td>10-310-1</td>
<td>&nbsp;</td>
<tr>
<td>QFill3</td>
<td>&nbsp;</td>
<td>Genetix</td>
<td>X3050</td>
<td>&nbsp;</td>
<tr>
<td>Bleach</td>
<td>&nbsp;</td>
<td>Javex</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Ethanol</td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>E7023</td>
<td>&nbsp;</td>
<tr>
<td>15 mL centrifuge tubes</td>
<td>&nbsp;</td>
<td>Fisher-Corning</td>
<td>430052</td>
<td>&nbsp;</td>
<tr>
<td>QPix colony picker</td>
<td>&nbsp;</td>
<td>Genetix</td>
<td>QPix2</td>
<td>&nbsp;</td>
<tr>
<td>picking head (E. coli) </td>
<td>&nbsp;</td>
<td>Genetix</td>
<td>X4006</td>
<td>&nbsp;</td>		</tbody>
		</table>
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large insert environmental genomic library production

Doğada mikropların büyük bir çoğunluğu şu anda, geleneksel tarım yöntemleri erişilemez kalır. Geçtiğimiz on yıl boyunca, kültür-bağımsız çevre genomik (<em&gt; Yani</em&gt; Metagenomic) yaklaşımları, araştırmacılar, bu kültür ortamında doğrudan yerli mikrobiyal toplulukların genetik içeriği yakalayarak köprü sağlayan ortaya çıkmıştır. Bu amaçla, genomik DNA kütüphaneleri de olsa standart sanatsal laboratuar klonlama teknikleri kullanılarak inşa edilmektedir. Burada mevsimsel hipoksik fiyort dikey derinliği süreklilik elde edilen DNA ile büyük bir ekleme çevre genomik fosmid kütüphane yapım açıklar. Bu protokol doğrudan kıyı deniz suyu örnekleme [1] bağlı protokoller de dahil olmak üzere bir dizi bağlı mikrobiyal biyokütle, büyük hacimli filtrasyon [2] ve bir DNA ekstraksiyonu ve saflaştırma protokol [3]. Başlangıçta, yüksek kalitede genomik DNA 5-fosforile künt biter oluşturulması ile sona onarılmıştır. End-DNA tamir boyutu seçimi ve jel çıkarma, 30 ve 60 bin baz çiftinden (Kb) uzunluğu arasında DNA parçaları kurtarmak için yapılır pulsed-field jel elektroforezi (PFGE) tabi tutulur. Boyutu seçilen DNA PFGE jel matris uzak saflaştırılmış ve künt uç fosfataz tedavi fosmid CopyControl vektör pCC1 (Epicentre bağlandı.<a href="http://www.epibio.com/item.asp?ID=385"&gt; Http://www.epibio.com/item.asp?ID=385</a&gt;). PCC1 ve insert DNA Lineer concatemers sonradan faj dayanıklı sonraki enfeksiyonu ile lambda terminase faj parçacıkları içine paketlenmiş headfull<em&gt; E. coli</em&gt; Hücreler. Başarıyla transduced klonlar antibiyotik seçimi altında LB agar plaklarına kurtarıldı ve robot alarak otomatik bir koloni (Qpix2, GENETIX) kullanarak 384 plaka biçimi arşivlenir. Mevcut protokol Epicentre CopyControl Fosmid Kütüphane Üretim Seti de dahil olmak üzere çeşitli kaynaklardan çizer ve birden fazla araştırma grupları yayınlanan eserler [4-7]. Her adım, akılda en iyi uygulamalar ile sunulmuştur. Genel kütüphane üretim kalitesini ve verimliliğini artırmak için yürütme inceliklerini vurgulamak Mümkün olduğunda. Dahil pek çok kuluçka adımları olduğu gibi, fosmid kütüphane üretim ve otomatik koloni toplama tüm süreç en az 7-10 gün sürer. Ancak, protokol içinde belirtilen olası birkaç durak noktaları vardır.

Watch this Scientific Journal Video about Large Insert Environmental Genomic Library Production at JoVE.com

Large Insert Environmental Genomic Library Production

Mevsimsel hipoksik fiyort dikey derinliği süreklilik çevre genomik DNA izole bir fosmid kütüphane inşaatı açıklanmıştır. Çıkan klon kütüphanesi 384-kuyucuğu içine aldı ve mansap sıralama ve fonksiyonel tarama, otomatik bir koloni toplama sistemi uygulama tarafından arşivlenir.

Büyük Ekle Çevre Genomik Kütüphane Üretim

The vast majority of microbes in nature currently remain inaccessible to traditional cultivation methods. Over the past decade, culture-independent ...

large-insert-environmental-genomic-library-production

Research

JoVE Journal

Biology

15.9K Görüntüleme.  University of British Columbia - UBC. Mevsimsel hipoksik fiyort dikey derinliği süreklilik çevre genomik DNA izole bir fosmid kütüphane inşaatı açıklanmıştır. Çıkan klon kütüphanesi 384-kuyucuğu içine aldı ve mansap sıralama ve fonksiyonel tarama, otomatik bir koloni toplama sistemi uygulama tarafından arşivlenir.

Video: Large Insert Environmental Genomic Library Production

Large-Scale Screens of Metagenomic Libraries

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation. Generating a streamlined procedure for creating and screening metagenomic libraries is therefore useful for efficient high-throughput investigations into the genetic and metabolic properties of uncultured microbial assemblages. Here, key protocols are presented on video, which we propose is the most useful format for accurately describing a long process that alternately depends on robotic instrumentation and (human) manual interventions. First, we employed robotics to spot library clones onto high-density macroarray membranes, each of which can contain duplicate colonies from twenty-four 384-well library plates. Automation is essential for this procedure not only for accuracy and speed, but also due to the miniaturization of scale required to fit the large number of library clones into highly dense spatial arrangements. Once generated, we next demonstrated how the macroarray membranes can be screened for genes of interest using modified versions of standard protocols for probe labeling, membrane hybridization, and signal detection. We complemented the visual demonstration of these procedures with detailed written descriptions of the steps involved and the materials required, all of which are available online alongside the video.

Metagenomic Kütüphaneler Büyük Ölçekli Ekranlar

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation.  Generating a ...

Biyoloji

Isolation of Genomic DNA from Mouse Tails

Fare Tails Genomik DNA izolasyonu

Technical Demonstration of 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 advances in this technology have enabled high resolution comparison of whole genomes for the identification of genetic alterations in cancer and other genetic diseases 2. The Sub-Megabase Resolution Tiling-set array (or SMRT) array is comprised of a set of approximately thirty thousand overlapping bacterial artificial chromosome (BAC) clones that span the human genome in ~100 kilobase pair (kb) segments 2. These BAC targets are individually synthesized and spotted in duplicate on a single glass slide 2-4. Array CGH is based on the principle of competitive hybridization. Sample and reference DNA are differentially labeled with Cyanine-3 and Cyanine-5 fluorescent dyes, and co-hybridized to the array. After an incubation period the unbound samples are washed from the slide and the array is imaged. A freely available custom software package called SeeGH (www.flintbox.ca) is used to process the large volume of data collected - a single experiment generates 53,892 data points. SeeGH visualizes the log2 signal intensity ratio between the 2 samples at each BAC target which is vertically aligned with chromosomal position 5,6. The SMRT array can detect alterations as small as 50 kb in size 7. The SMRT array can detect a variety of DNA rearrangement events including DNA gains, losses, amplifications and homozygous deletions. A unique advantage of the SMRT array is that one can use DNA isolated from formalin fixed paraffin embedded samples. When combined with the low input requirements of unamplified DNA (25-100ng) this allows profiling of precious samples such as those produced by microdissection 7,8. This is attributed to the large size of each BAC hybridization target that allows the binding of sufficient labeled samples to produce signals for detection. Another advantage of this platform is the tolerance of tissue heterogeneity, decreasing the need for tedious tissue microdissection 8. This video protocol is a step-by-step tutorial from labeling the input DNA through to signal acquisition for the whole genome tiling path SMRT array.

This video is a technical demonstration of the hybridization protocol for whole genome tiling path array CGH, which scans the entire human genome using only 25-100 ng of DNA that can be isolated from a variety of sources, including archival formalin fixed material.

Tüm Genom Dizisi Karşılaştırmalı Genomik Hibridizasyon Teknik gösteri

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 ...

Lentivirus Production

RNA interference (RNAi) is a system of gene silencing in living cells. In RNAi, genes homologous in sequence to short interfering RNAs (siRNA) are silenced at the post-transcriptional state. Short hairpin RNAs, precursors to siRNA, can be expressed using lentivirus, allowing for RNAi in a variety of cell types. Lentiviruses, such as the Human Immunodeficiency Virus, are capable to infecting both dividing and non-dividing cells. We will describe a procedure which to package lentiviruses. Packaging refers to the preparation of competent virus from DNA vectors. Lentiviral vector production systems are based on a 'split' system, where the natural viral genome has been split into individual helper plasmid constructs. This splitting of the different viral elements into four separate vectors diminishes the risk of creating a replication-capable virus by adventitious recombination of the lentiviral genome. Here, a vector containing the shRNA of interest and three packaging vectors (p-VSVG, pRSV, pMDL) are transiently transfected into human 293 cells. After at least a 48-hour incubation period, the virus containing supernatant is harvested and concentrated. Finally, virus titer is determined by reporter (fluorescent) expression with a flow cytometer.

To make lentiviruses, DNA vectors are transfected into human 293 cells. After harvest and concentrating the supernatant, virus titer is determined by fluorescence expression with a flow cytometer.

Lentivirüs Üretim

RNA interference (RNAi) is a system of gene silencing in living cells. In RNAi, genes homologous in sequence to short interfering RNAs (siRNA) are ...

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in their nucleotide composition and consist of a complex mosaic of sequence patterns. These patterns include so-called Mid-Range Inhomogeneity (MRI) regions -- sequences 30-10000 nucleotides in length that are enriched by a particular base or combination of bases (e.g. (G+T)-rich, purine-rich, etc.). MRI regions are associated with unusual (non-B-form) DNA structures that are often involved in regulation of gene expression, recombination, and other genetic processes (Fedorova &amp; Fedorov 2010). The existence of a strong fixation bias within MRI regions against mutations that tend to reduce their sequence inhomogeneity additionally supports the functionality and importance of these genomic sequences (Prakash et al. 2009).
Here we demonstrate a freely available Internet resource -- the Genomic MRI program package -- designed for computational analysis of genomic sequences in order to find and characterize various MRI patterns within them (Bechtel et al. 2008). This package also allows generation of randomized sequences with various properties and level of correspondence to the natural input DNA sequences. The main goal of this resource is to facilitate examination of vast regions of non-coding DNA that are still scarcely investigated and await thorough exploration and recognition.

We present a public computational web site for the analysis of genomic sequences. It detects DNA sequence patterns with various non-random nucleotide compositions. This resource also generates randomized sequences with diverse levels of complexity.

MR Genomik - Sıra Desenler Genomik DNA içinde incelenmesi için Kamu Kaynak

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in ...

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.

Barkodlu Maya Kütüphaneler Rekabet Genomik Ekranlar

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

MISSION LentiPlex Pooled shRNA Library Screening in Mammalian Cells

RNA interference (RNAi) is an intrinsic cellular mechanism for the regulation of gene expression. Harnessing the innate power of this system enables us to knockdown gene expression levels in loss of gene function studies.
There are two main methods for performing RNAi. The first is the use of small interfering RNAs (siRNAs) that are chemically synthesized, and the second utilizes short-hairpin RNAs (shRNAs) encoded within plasmids 1. The latter can be transfected into cells directly or packaged into replication incompetent lentiviral particles. The main advantages of using lentiviral shRNAs is the ease of introduction into a wide variety of cell types, their ability to stably integrate into the genome for long term gene knockdown and selection, and their efficacy in conducting high-throughput loss of function screens. To facilitate this we have created the LentiPlex pooled shRNA library.
The MISSION LentiPlex Human shRNA Pooled Library is a genome-wide lentiviral pool produced using a proprietary process. The library consists of over 75,000 shRNA constructs from the TRC collection targeting 15,000+ human genes 2. Each library is tested for shRNA representation before product release to ensure robust library coverage. The library is provided in a ready-to-use lentiviral format at titers of at least 5 x 108 TU/ml via p24 assay and is pre-divided into ten subpools of approximately 8,000 shRNA constructs each. Amplification and sequencing primers are also provided for downstream target identification.
Previous studies established a synergistic antitumor activity of TRAIL when combined with Paclitaxel in A549 cells, a human lung carcinoma cell line 3, 4. In this study we demonstrate the application of a pooled LentiPlex shRNA library to rapidly conduct a positive selection screen for genes involved in the cytotoxicity of A549 cells when exposed to TRAIL and Paclitaxel. One barrier often encountered with high-throughput screens is the cost and difficulty in deconvolution; we also detail a cost-effective polyclonal approach utilizing traditional sequencing.

Here we use a human LentiPlex pooled library and traditional sequencing methods to identify gene targets promoting cell survival. We demonstrate how to set up and deconvolute a LentiPlex screen and validate the results.

MİSYON LentiPlex Memeli Hücreleri shRNA Kütüphane Tarama Pooled

RNA interference (RNAi) is an intrinsic cellular mechanism for the regulation of gene expression. Harnessing the innate power of this system enables us to ...

Selective Capture of 5-hydroxymethylcytosine from Genomic DNA

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene expression, maintenance of genome integrity, parental imprinting, X-chromosome inactivation, regulation of development, aging, and cancer1. Recently, the presence of an oxidized 5-mC, 5-hydroxymethylcytosine (5-hmC), was discovered in mammalian cells, in particular in embryonic stem (ES) cells and neuronal cells2-4. 5-hmC is generated by oxidation of 5-mC catalyzed by TET family iron (II)/&alpha;-ketoglutarate-dependent dioxygenases2, 3. 5-hmC is proposed to be involved in the maintenance of embryonic stem (mES) cell, normal hematopoiesis and malignancies, and zygote development2, 5-10. To better understand the function of 5-hmC, a reliable and straightforward sequencing system is essential. Traditional bisulfite sequencing cannot distinguish 5-hmC from 5-mC11. To unravel the biology of 5-hmC, we have developed a highly efficient and selective chemical approach to label and capture 5-hmC, taking advantage of a bacteriophage enzyme that adds a glucose moiety to 5-hmC specifically12.
Here we describe a straightforward two-step procedure for selective chemical labeling of 5-hmC. In the first labeling step, 5-hmC in genomic DNA is labeled with a 6-azide-glucose catalyzed by &beta;-GT, a glucosyltransferase from T4 bacteriophage, in a way that transfers the 6-azide-glucose to 5-hmC from the modified cofactor, UDP-6-N3-Glc (6-N3UDPG). In the second step, biotinylation, a disulfide biotin linker is attached to the azide group by click chemistry. Both steps are highly specific and efficient, leading to complete labeling regardless of the abundance of 5-hmC in genomic regions and giving extremely low background. Following biotinylation of 5-hmC, the 5-hmC-containing DNA fragments are then selectively captured using streptavidin beads in a density-independent manner. The resulting 5-hmC-enriched DNA fragments could be used for downstream analyses, including next-generation sequencing.
Our selective labeling and capture protocol confers high sensitivity, applicable to any source of genomic DNA with variable/diverse 5-hmC abundances. Although the main purpose of this protocol is its downstream application (i.e., next-generation sequencing to map out the 5-hmC distribution in genome), it is compatible with single-molecule, real-time SMRT (DNA) sequencing, which is capable of delivering single-base resolution sequencing of 5-hmC.

Described is a two-step labeling process using &beta;-glucosyltransferase (&beta;-GT) to transfer an azide-glucose to 5-hmC, followed by click chemistry to transfer a biotin linker for easy and density-independent enrichment. This efficient and specific labeling method enables enrichment of 5-hmC with extremely low background and high-throughput epigenomic mapping via next-generation sequencing.

Genomik DNA 5-hydroxymethylcytosine seçici Yakalama

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene ...

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.

Genomik Kopya Sayısı Variantların Algılama için dizi Karşılaştırmalı Genomik Hibridizasyon (CGH Array)

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

3' End Sequencing Library Preparation with A-seq2

Studies in the last decade have revealed a complex and dynamic variety of pre-mRNA cleavage and polyadenylation reactions. mRNAs with long 3&#39; untranslated regions (UTRs) are generated in differentiated cells whereas proliferating cells preferentially express transcripts with short 3&#39;UTRs. We describe the A-seq protocol, now at its second version, which was developed to map polyadenylation sites genome-wide and study the regulation of pre-mRNA 3&#39; end processing. Also this current protocol takes advantage of the polyadenylate (poly(A)) tails that are added during the biogenesis of most mammalian mRNAs to enrich for fully processed mRNAs. A DNA adaptor with deoxyuracil at its fourth position allows the precise processing of mRNA 3&#39; end fragments for sequencing. Not including the cell culture and the overnight ligations, the protocol requires about 8 h hands-on time. Along with it, an easy-to-use software package for the analysis of the derived sequencing data is provided. A-seq2 and the associated analysis software provide an efficient and reliable solution to the mapping of pre-mRNA 3&#39; ends in a wide range of conditions, from 106 or fewer cells.

This protocol describes a method for mapping pre-mRNA 3&#39; end processing sites.