هذا العمل كان يدعمها في "المعاهد الوطنية للصحة": R21 المعاهد الوطنية للصحة EB021870-01A1 و "منحة مشروع بحوث جبهة الخلاص الوطني": 1517110.

<ol>
	<li>Fields, S., Song, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+genetic+system+to+detect+protein-protein+interactions.">A novel genetic system to detect protein-protein interactions.</a> Nature. 340 (6230), 245-246 (1989).</li><li>Rajagopala, S. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+the+Protein-Protein+Interactome+Networks+Using+Yeast+Two-Hybrid+Screens.">Mapping the Protein-Protein Interactome Networks Using Yeast Two-Hybrid Screens.</a> Advances in Experimental Medicine and Biology. 883, 187-214 (2015).</li><li>Weimann, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Y2H-seq+approach+defines+the+human+protein+methyltransferase+interactome.">A Y2H-seq approach defines the human protein methyltransferase interactome.</a> Nature Methods. 10 (4), 339-342 (2013).</li><li>Yachie, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pooled-matrix+protein+interaction+screens+using+Barcode+Fusion+Genetics.">Pooled-matrix protein interaction screens using Barcode Fusion Genetics.</a> Molecular Systems Biology. 12 (4), 863 (2016).</li><li>Trigg, S. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CrY2H-seq:+a+massively+multiplexed+assay+for+deep-coverage+interactome+mapping.">CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.</a> Nature Methods. , (2017).</li><li>Pashkova, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DEEPN+as+an+Approach+for+Batch+Processing+of+Yeast+2-Hybrid+Interactions.">DEEPN as an Approach for Batch Processing of Yeast 2-Hybrid Interactions.</a> Cell Reports. 17 (1), 303-315 (2016).</li><li>Kim, D., Langmead, B., Salzberg, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HISAT:+a+fast+spliced+aligner+with+low+memory+requirements.">HISAT: a fast spliced aligner with low memory requirements.</a> Nature Methods. 12 (4), 357-360 (2015).</li><li>Reinert, K., Langmead, B., Weese, D., Evers, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alignment+of+Next-Generation+Sequencing+Reads.">Alignment of Next-Generation Sequencing Reads.</a> Annual Review of Genomics and Human Genetics. 16, 133-151 (2015).</li><li>Pertea, M., Kim, D., Pertea, G. M., Leek, J. T., Salzberg, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcript-level+expression+analysis+of+RNA-seq+experiments+with+HISAT,+StringTie+and+Ballgown.">Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.</a> Nature Protocols. 11 (9), 1650-1667 (2016).</li><li>Conesa, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+survey+of+best+practices+for+RNA-seq+data+analysis.">A survey of best practices for RNA-seq data analysis.</a> Genome Biology. 17, 13 (2016).</li></ol>

الكتاب لا تمت بصلة إلى الكشف عن

جناح البرامج المشروحة هنا يسمح أحد لمعالجة وتحليل بيانات تسلسل الحمض النووي الإنتاجية العالية من تجربة ديبن تماما. البرنامج الأول الذي استخدم هو MAPster، الذي يأخذ على ما يلي تسلسل الحمض النووي في الملفات القياسية فستق وخرائط موقفهم على مرجع الحمض النووي للتجهيز النهائي بمجموعة كاملة من ال?...

نهج واحد لاكتشاف تفاعلات البروتين هو الإنزيم (Y2H) 2-الهجين الخميرة، الذي يستغل هندسيا خلايا الخميرة التي تنمو فقط عندما وتين اهتمام بربط جزء من شريك المتفاعلة1. الآن يمكن أن يتم الكشف عن عدة Y2H التفاعلات مع مساعدة ضخمة يسلسل الفائق موازية. العديد من الأشكال وقد تم وصف2،3،،من45 بما في ذلك وضعنا وتزرع فيها السكان دفعة واحدة في ظل الظروف التي حدد للخميرة التي تحتوي على البلازميدات التي تنتج إيجابية التفاعل Y2H6. سير العمل نحن البلدان المتقدمة النمو، يسمى ديبن (التخصيب الحيوي لشبكات التقييم من البروتين)، ويحدد إينتيراكتوميس التفاضلية من نفس مكتبات فريسة لتحديد البروتينات التي تتفاعل مع واحد من البروتين (أو المجال) مقابل. بروتين آخر أو مجال المسخ كونفورماتيونالي متميزة. إحدى الخطوات الرئيسية في سير العمل هذا هو التجهيز السليم وتحليل بيانات تسلسل الحمض النووي. يمكن أن تكون بعض المعلومات المستقاة بمجرد إحصاء عدد القراءات لكل الجينات سواء قبل أو بعد التحديد التفاعلات Y2H بطريقة مشابهة لتجربة تسلسل الحمض النووي الريبي. ومع ذلك، يمكن استخراج معلومات متعمقة أكثر بكثير من مجموعات البيانات هذه بما في ذلك المعلومات المتعلقة بالمجال الفرعي بروتين معين التي قادرة على إنتاج تفاعل Y2H. وباﻹضافة إلى ذلك، بينما النهج ديبن الذي قيمة، تحليل العديد من عينة replicates يمكن أن تكون مرهقة ومكلفة. هو التخفيف من حدة هذه المشكلة باستخدام نموذج إحصائي تم تطويره خصيصا لمجموعات البيانات ديبن حيث هو عدد replicates محدودة6. لجعل معالجة وتحليل مجموعات البيانات تسلسل الحمض النووي موثوق بها وكاملة وقوية وموجودا للمحققين دون الخبرة المعلوماتية الحيوية، قمنا بتطوير مجموعة من البرامج التي تغطي كافة الخطوات للتحليل.
ويشمل هذا الجناح من البرامج القائمة بذاتها التي يتم تشغيلها على أجهزة كمبيوتر سطح المكتب MAPster وديبن و Stat_Maker. MAPster هو واجهة مستخدم الرسومية التي يسمح كل ملف فستق في قائمة الانتظار لرسم خرائط الجينوم استخدام برنامج HISAT27، إنتاج ملف.sam قياسية للاستخدام في تطبيقات المتلقين للمعلومات. وقد ديبن عدة وحدات. وهو يعين والتهم ما يلي المقابلة للجينات خاصة مماثلة للقياس الكمي نوع تسلسل الحمض النووي الريبي استخدام الوحدة النمطية 'العد الجينات'. كما تستخرج في تسلسل المقابلة على مفترق الطرق بين المجال النسخي Gal4 وتسلسل فريسة وجمع موقف تلك الوصلات للسماح بعمليات التفتيش بمقارنة الجداول والرسوم البيانية (باستخدام الوحدة النمطية 'Junction_Make') يسمح الوحدة النمطية 'Blast_Query' التفتيش سهلة، كوانتيتيشن، ومقارنة التسلسلات تقاطع مفرق Gal4. تقييم Stat_Maker على ما يلي كل الجينات إثراء البيانات إحصائيا كوسيلة لتحديد أولويات المحتمل Y2H مرات. وهنا، نحن تصف كيفية استخدام هذه البرامج لتحليل تسلسل الحمض النووي تجربة البيانات من Y2H ديبن الكامل. تتوفر إصدارات ديبن لتشغيلها على أنظمة الكمبيوتر، ماك و لينكس. برامج أخرى مثل برنامج رسم الخرائط MAPster ووحدة الإحصاء ديبن Stat_Maker تعتمد على subroutines التي تعمل تحت Unix وتتوفر فقط على أنظمة Mac و linux.

<table>
	<tbody>
		<tr>
			<td>Mapster</td>
			<td></td>
			<td></td>
			<td>https://github.com/emptyewer/MAPster/releases</td>
		</tr>
		<tr>
			<td>DEEPN software</td>
			<td></td>
			<td></td>
			<td>https://github.com/emptyewer/DEEPN/releases</td>
		</tr>
		<tr>
			<td>Statmaker</td>
			<td></td>
			<td></td>
			<td>https://github.com/emptyewer/DEEPN/releases</td>
		</tr>
		<tr>
			<td>Minimum computer system</td>
			<td>Apple</td>
			<td></td>
			<td>Mac Intel Core i5 or better</td>
		</tr>
		<tr>
			<td></td>
			<td>-</td>
			<td></td>
			<td>4 Gb RAM or better</td>
		</tr>
		<tr>
			<td></td>
			<td>-</td>
			<td></td>
			<td>500 Gb Disk spce or better</td>
		</tr>
		<tr>
			<td></td>
			<td>-</td>
			<td></td>
			<td>OS 10.10 or higher</td>
		</tr>
		<tr>
			<td></td>
			<td>Dell</td>
			<td></td>
			<td>Intel i5-7400 or better</td>
		</tr>
		<tr>
			<td></td>
			<td>-</td>
			<td></td>
			<td>4 Gb RAM or better</td>
		</tr>
		<tr>
			<td></td>
			<td>-</td>
			<td></td>
			<td>500 Gb Disk spce or better</td>
		</tr>
		<tr>
			<td></td>
			<td>-</td>
			<td></td>
			<td>Windows 7 or higher</td>
		</tr>
	</tbody>
</table>

informatic analysis of sequence data from batch yeast 2-hybrid screens

ونحن قد تكيفت المقايسة 2-الهجين الخميرة في الوقت نفسه كشف العشرات من تفاعلات البروتين عابرة وثابتة ضمن شاشة واحدة تستخدم الفائق قصيرة-قراءة تسلسل الحمض النووي. مجموعات البيانات الناتجة عن تسلسل يمكن أن تتبع ما الجينات في عدد سكان التي هي إثراء من خلال التحديد للتفاعلات الإيجابية الخميرة 2-الهجين، بل أيضا إعطاء معلومات مفصلة حول المجالات الفرعية ذات الصلة من البروتينات كافية للتفاعل. وهنا يصف لنا مجموعة كاملة من البرامج القائمة بذاتها التي تسمح لغير الخبراء لأداء جميع المعلوماتية الحيوية والخطوات الإحصائية لمعالجة وتحليل ملفات فستق تسلسل الحمض النووي من تحليل 2-هجين خميرة دفعة. خطوات المعالجة المشمولة بهذه البرامج وتشمل: ما يلي تسلسل 1) رسم الخرائط والعد المقابلة لكل مرشح البروتين المشفرة داخل مكتبة فريسة 2-الهجين خميرة؛ 2) برنامج تحليل الإحصائي الذي يقيم في التشكيلات الجانبية للإثراء؛ و 3) أدوات لدراسة الإطار متعدية الجنسيات والموقف داخل منطقة الترميز لكل بلازميد المخصب الذي يشفر البروتينات المتفاعلة للفائدة.

تعيين البيانات فستق: الخطوة الأولى في عمليا جميع خ ع تطبيقاته ديبن الإخراج الأولى هو ملف من ما يلي تسلسل قصيرة التي يجب تعيينها بالمحاذاة للجينوم، ترانسكريبتوميك، أو أخرى مرجعية الحمض النووي8. في الآونة الأخيرة، تم تطوير هذا البرنامج المحاذاة HISAT2...

Watch this Scientific Journal Video about Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens at JoVE.com

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

التسلسل بالغ السكان الخميرة المختارة للتفاعلات الإيجابية الخميرة 2-الهجين يحتمل أن تكون غلة ثروة معلومات حول التفاعل شريك البروتينات. هنا، يمكننا وصف تشغيل أدوات المعلوماتية الحيوية المحددة والبرامج المحدثة المخصصة لتحليل بيانات تسلسل من هذه الشاشات.

تحليل بيانات تسلسل من دفعة الخميرة 2-الهجين شاشات المعلوماتي

We have adapted the yeast 2-hybrid assay to simultaneously uncover dozens of transient and static protein interactions within a single screen utilizing ...

informatic-analysis-of-sequence-data-from-batch-yeast-2-hybrid-screens

Research

JoVE Journal

Genetics

7.1K Views.  University of Iowa. التسلسل بالغ السكان الخميرة المختارة للتفاعلات الإيجابية الخميرة 2-الهجين يحتمل أن تكون غلة ثروة معلومات حول التفاعل شريك البروتينات. هنا، يمكننا وصف تشغيل أدوات المعلوماتية الحيوية المحددة والبرامج المحدثة المخصصة لتحليل بيانات تسلسل من هذه الشاشات.

Video: Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation

The transfer of genetic material by bacterial conjugation is a process that takes place via complexes formed by specific transfer proteins. In Escherichia coli, these transfer proteins make up a DNA transfer machinery known as the mating pair formation, or DNA transfer complex, which facilitates conjugative plasmid transfer. The objective of this paper is to provide a method that can be used to determine the role of a specific transfer protein that is involved in conjugation using a series of deletions and/or point mutations in combination with mating assays. The target gene is knocked out on the conjugative plasmid and is then provided in trans through the use of a small recovery plasmid harboring the target gene. Mutations affecting the target gene on the recovery plasmid can reveal information about functional aspects of the target protein that result in the alteration of mating efficiency of donor cells harboring the mutated gene. Alterations in mating efficiency provide insight into the role and importance of the particular transfer protein, or a region therein, in facilitating conjugative DNA transfer. Coupling this mating assay with detailed three-dimensional structural studies will provide a comprehensive understanding of the function of the conjugative transfer protein as well as provide a means for identifying and characterizing regions of protein-protein interaction.

Here, we present a protocol to knockout a gene of interest involved in plasmid conjugation and subsequently analyze the impact of its absence using mating assays. The function of the gene is further explored to a specific region of its sequence using deletion or point mutations.

اقترانية التزاوج فحوصات لتحليل تسلسل محدد من البروتينات نقل تشارك في الإقتران البكتيرية

The transfer of genetic material by bacterial conjugation is a process that takes place via complexes formed by specific transfer proteins. In Escherichia ...

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets. However, for first-time users and bioinformatics' amateurs, self-learning and familiarization with these platforms can be time-consuming and daunting. We describe a straightforward workflow that will help C. elegans researchers to isolate worm RNA, conduct an RNA-Seq experiment and analyze the data using Galaxy and DAVID platforms. This protocol provides stepwise instructions for using the various Galaxy modules for accessing raw NGS data, quality-control checks, alignment, and differential gene expression analysis, guiding the user with parameters at every step to generate a gene list that can be screened for enrichment of gene classes or biological processes using DAVID. Overall, we anticipate that this article will provide information to C. elegans researchers undertaking RNA-Seq experiments for the first time as well as frequent users running a small number of samples.

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Galaxy and DAVID have emerged as popular tools that allow investigators without bioinformatics training to analyze and interpret RNA-Seq data. We describe a protocol for C. elegans researchers to perform RNA-Seq experiments, access and process the dataset using Galaxy and obtain meaningful biological information from the gene lists using DAVID.

تحليل Transcriptomic من<em&gt; C</em&gt;.<em&gt; ايليجانس</em&gt; RNA تسلسل البيانات من خلال جناح سهرة على مشروع غالاكسي

Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged ...

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral gene therapy studies, IS assays, in combination with next-generation sequencing, have been used as a cell-tracking tool to characterize clonal stem cell populations sharing the same IS. For the accurate comparison of repopulating stem cell clones within and across different samples, the detection sensitivity, data reproducibility, and high-throughput capacity of the assay are among the most important assay qualities. This work provides a detailed protocol and data analysis workflow for bidirectional IS analysis. The bidirectional assay can simultaneously sequence both upstream and downstream vector-host junctions. Compared to conventional unidirectional IS sequencing approaches, the bidirectional approach significantly improves IS detection rates and the characterization of integration events at both ends of the target DNA. The data analysis pipeline described here accurately identifies and enumerates identical IS sequences through multiple steps of comparison that map IS sequences onto the reference genome and determine sequencing errors. Using an optimized assay procedure, we have recently published the detailed repopulation patterns of thousands of Hematopoietic Stem Cell (HSC) clones following transplant in rhesus macaques, demonstrating for the first time the precise time point of HSC repopulation and the functional heterogeneity of HSCs in the primate system. The following protocol describes the step-by-step experimental procedure and data analysis workflow that accurately identifies and quantifies identical IS sequences.

This manuscript describes the experimental procedure and software analysis for a bidirectional integration site assay that can simultaneously analyze upstream and downstream vector-host junction DNA. Bidirectional PCR products can be used for any downstream sequencing platform. The resulting data are useful for a high-throughput, quantitative comparison of integrated DNA targets.

موقع التكامل ثنائي الاتجاه للفيروسات القهقرية منهجية ير والتحليل الكمي للبيانات سير العمل

Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral ...

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

The analysis of global gene expression changes is a valuable tool for identifying novel pathways underlying observed phenotypes. The zebrafish is an excellent model for rapid assessment of whole transcriptome from whole animal or individual cell populations due to the ease of isolation of RNA from large numbers of animals. Here a protocol for global gene expression analysis in zebrafish embryos using RNA sequencing (RNASeq) is presented. We describe preparation of RNA from whole embryos or from cell populations obtained using cell sorting in transgenic animals. We also describe an approach for analysis of RNASeq data to identify enriched pathways and Gene Ontology (GO) terms in global gene expression data sets. Finally, we provide a protocol for validation of gene expression changes using quantitative reverse transcriptase PCR (qRT-PCR). These protocols can be used for comparative analysis of control and experimental sets of zebrafish to identify novel gene expression changes, and provide molecular insight into phenotypes of interest.

This protocol presents an approach for whole transcriptome analysis from zebrafish embryos, larvae, or sorted cells. We include isolation of RNA, pathway analysis of RNASeq data, and qRT-PCR-based validation of gene expression changes.

نموذج إعداد وتحليل البيانات التعبير الجيني على أساس رناسيق من الزرد

The analysis of global gene expression changes is a valuable tool for identifying novel pathways underlying observed phenotypes. The zebrafish is an ...

Single Molecule Fluorescence In Situ Hybridization (smFISH) Analysis in Budding Yeast Vegetative Growth and Meiosis

Single molecule fluorescence in situ hybridization (smFISH) is a powerful technique to study gene expression in single cells due to its ability to detect and count individual RNA molecules. Complementary to deep sequencing-based methods, smFISH provides information about the cell-to-cell variation in transcript abundance and the subcellular localization of a given RNA. Recently, we have used smFISH to study the expression of the gene&#160;NDC80&#160;during meiosis in budding yeast, in which two transcript isoforms exist and the short transcript isoform has its entire sequence shared with the long isoform. To confidently identify each transcript isoform, we optimized known smFISH protocols and obtained high consistency and quality of smFISH data for the samples acquired during budding yeast meiosis. Here, we describe this optimized protocol, the criteria that we use to determine whether high quality of smFISH data is obtained, and some tips for implementing this protocol in&#160;other yeast strains and growth conditions.

Single Molecule Fluorescence In Situ Hybridization smFISH Analysis in Budding Yeast Vegetative Growth and Meiosis

This single molecule fluorescence in situ hybridization protocol is optimized to quantify the number of RNA molecules in budding yeast during vegetative growth and meiosis.

التهجين في الموقع Fluorescence جزيء واحد (سمفيش) التحليل في مهدها الخميرة النمو الخضري والانقسام الاختزالي

Single molecule fluorescence in situ hybridization (smFISH) is a powerful technique to study gene expression in single cells due to its ability to detect ...

Mating-based Overexpression Library Screening in Yeast

Budding yeast has been widely used as a model in studying proteins associated with human diseases. Genome-wide genetic screening is a powerful tool commonly used in yeast studies. The expression of a number of neurodegenerative disease-associated proteins in yeast causes cytotoxicity and aggregate formation, recapitulating findings seen in patients with these disorders. Here, we describe a method for screening a yeast model of the Amyotrophic Lateral Sclerosis-associated protein FUS for modifiers of its toxicity. Instead of using transformation, this new screening platform relies on the mating of yeast to introduce an arrayed library of plasmids into the yeast model. The mating method has two clear advantages: first, it is highly efficient; second, the pre-transformed arrayed library of plasmids can be stored for long-term as a glycerol stock, and quickly applied to other screens without the labor-intensive step of transformation into the yeast model each time. We demonstrate how this method can successfully be used to screen for genes that modify the toxicity of FUS.

This article presents a mating-based method to facilitate overexpression screening in budding yeast using an arrayed plasmid library.

فحص مكتبة Overexpression المستندة إلى التزاوج في الخميرة

Budding yeast has been widely used as a model in studying proteins associated with human diseases. Genome-wide genetic screening is a powerful tool ...

Novel Sequence Discovery by Subtractive Genomics

Subtractive genomics can be used in any research where the goal is to identify the sequence of a gene, protein, or general region that is embedded in a larger genomic context. Subtractive genomics enables a researcher to isolate a target sequence of interest (T) by comprehensive sequencing and subtracting out known genetic elements (reference, R). The method can be used to identify novel sequences such as mitochondria, chloroplasts, viruses, or germline restricted chromosomes, and is particularly useful when T cannot be easily isolated from R. Beginning with the comprehensive genomic data (R + T), the method uses Basic Local Alignment Search Tool (BLAST) against a reference sequence, or sequences, to remove the matching known sequences (R), leaving behind the target (T). For subtraction to work best, R should be a relatively complete draft that is missing T. Since sequences remaining after subtraction are tested through quantitative Polymerase Chain Reaction (qPCR), R does not need to be complete for the method to work. Here we link computational steps with experimental steps into a cycle that can be iterated as needed, sequentially removing multiple reference sequences and refining the search for T. The advantage of subtractive genomics is that a completely novel target sequence can be identified even in cases in which physical purification is difficult, impossible, or expensive. A drawback of the method is finding a suitable reference for subtraction and obtaining T-positive and negative samples for qPCR testing. We describe our implementation of the method in the identification of the first gene from the germline-restricted chromosome of zebra finch. In that case computational filtering involved three references (R), sequentially removed over three cycles: an incomplete genomic assembly, raw genomic data, and transcriptomic data.

The purpose of this protocol is to use a combination of computational and bench research to find novel sequences that cannot be easily separated from a co-purifying sequence, which may be only partially known.

اكتشاف رواية تسلسل الجينوم مطروح

Subtractive genomics can be used in any research where the goal is to identify the sequence of a gene, protein, or general region that is embedded in a ...

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

Identifying the sets of transcription factors (TFs) that regulate each human gene is a daunting task that requires integrating numerous experimental and computational approaches. One such method is the yeast one-hybrid (Y1H) assay, in which interactions between TFs and DNA regions are tested in the milieu of the yeast nucleus using reporter genes. Y1H assays involve two components: a &#8216;DNA-bait&#8217; (e.g., promoters, enhancers, silencers, etc.) and a &#8216;TF-prey,&#8217; which can be screened for reporter gene activation. Most published protocols for performing Y1H screens are based on transforming TF-prey libraries or arrays into DNA-bait yeast strains. Here, we describe a pipeline, called enhanced Y1H (eY1H) assays, where TF-DNA interactions are interrogated by mating DNA-bait strains with an arrayed collection of TF-prey strains using a high density array (HDA) robotic platform that allows screening in a 1,536 colony format. This allows for a dramatic increase in throughput (60 DNA-bait sequences against &#62;1,000 TFs takes two weeks per researcher) and reproducibility. We illustrate the different types of expected results by testing human promoter sequences against an array of 1,086 human TFs, as well as examples of issues that can arise during screens and how to troubleshoot them.

Here, we present an enhanced yeast one-hybrid screening protocol to identify the transcription factors (TFs) that can bind to a human DNA region of interest. This method uses a high-throughput screening pipeline that can interrogate the binding of &#62;1,000 TFs in a single experiment.

شاشات الهجين واحد الخميرة المحسنة لتحديد عامل النسخ ملزمة لتسلسل الحمض النووي البشري

Identifying the sets of transcription factors (TFs) that regulate each human gene is a daunting task that requires integrating numerous experimental and ...

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Genome editing using the CRISPR-Cas system has vastly advanced the ability to precisely edit the genomes of various organisms. In the context of mammalian cells, this technology represents a novel means to perform genome-wide genetic screens for functional genomics studies. Libraries of guide RNAs (sgRNA) targeting all open reading frames permit the facile generation of thousands of genetic perturbations in a single pool of cells that can be screened for specific phenotypes to implicate gene function and cellular processes in an unbiased and systematic way. CRISPR-Cas screens provide researchers with a simple, efficient, and inexpensive method to uncover the genetic blueprints for cellular phenotypes. Furthermore, differential analysis of screens performed in various cell lines and from different cancer types can identify genes that are contextually essential in tumor cells, revealing potential targets for specific anticancer therapies. Performing genome-wide screens in human cells can be daunting, as this involves the handling of tens of millions of cells and requires analysis of large sets of data. The details of these screens, such as cell line characterization, CRISPR library considerations, and understanding the limitations and capabilities of CRISPR technology during analysis, are often overlooked. Provided here is a detailed protocol for the successful performance of pooled genome-wide CRISPR-Cas9 based screens.

CRISPR-Cas9 technology provides an efficient method to precisely edit the mammalian genome in any cell type and represents a novel means to perform genome-wide genetic screens. A detailed protocol discussing the steps required for the successful performance of pooled genome-wide CRISPR-Cas9 screens is provided here.

الشاشات الوراثية المجمعة المستندة إلى كريسبر في خلايا الثدييات

Genome editing using the CRISPR-Cas system has vastly advanced the ability to precisely edit the genomes of various organisms. In the context of mammalian ...

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

A central goal of modern genetics is to understand how and why organisms in the wild differ in phenotype. To date, the field has advanced largely on the strength of linkage and association mapping methods, which trace the relationship between DNA sequence variants and phenotype across recombinant progeny from matings between individuals of a species. These approaches, although powerful, are not well suited to trait differences between reproductively isolated species. Here we describe a new method for genome-wide dissection of natural trait variation that can be readily applied to incompatible species. Our strategy, RH-seq, is a genome-wide implementation of the reciprocal hemizygote test. We harnessed it to identify the genes responsible for the striking high temperature growth of the yeast Saccharomyces cerevisiae relative to its sister species S. paradoxus. RH-seq utilizes transposon mutagenesis to create a pool of reciprocal hemizygotes, which are then tracked through a high-temperature competition via high-throughput sequencing. Our RH-seq workflow as laid out here provides a rigorous, unbiased way to dissect ancient, complex traits in the budding yeast clade, with the caveat that resource-intensive deep sequencing is needed to ensure genomic coverage for genetic mapping. As sequencing costs drop, this approach holds great promise for future use across eukaryotes.

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Reciprocal hemizygosity via sequencing (RH-seq) is a powerful new method to map the genetic basis of a trait difference between species. Pools of hemizygotes are generated by transposon mutagenesis and their fitness is tracked through competitive growth using high-throughout sequencing. Analysis of the resulting data pinpoints genes underlying the trait.

رسم الخرائط الوراثية للاختلافات التسامح الحراري بين أنواع الخميرة Saccharomyces عن طريق تحليل الهيميزيغوستي على نطاق الجينوم المتبادل

A central goal of modern genetics is to understand how and why organisms in the wild differ in phenotype. To date, the field has advanced largely on the ...