Name: transcriptomic analysis of c. elegans rna sequencing data through the tuxedo suite on the galaxy project
Uploaded: 2017-04-08T13:00:00.000+00:00
Duration: 10 min 19 s
Description: Watch this Scientific Journal Video about Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project at JoVE.com

作者想表达自己的感激之情谁开发银河和DAVID，从而取得NGS科学界广泛接受的实验室，团体和个人。在我们的生物信息学的培训，在匹兹堡大学的同事提供的帮助和建议是公认的。这项工作是由一个埃里森医学基金会新学者在老龄化奖（AG-NS-0879-12）和美国国立卫生研究院（R01AG051659），以股份公司的资助。

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在现代生物学银河测序平台的意义银河项目已成为帮助生物学家没有生物信息学培训，以处理和快速，高效地分析高通量测序数据的工具。曾经被视为一个艰巨的任务，这个公开可用的平台，取得了运行复杂的生物信息学算法来分析NGS数据的简单，可靠，简单的过程。除了托管范围广泛的生物信息学工具，成功的关键银河也是它的用户界面的该鞋带复杂测序分析的各个方面一起...

人类基因组的测序首先，执行使用弗雷德·桑格的双脱氧核苷酸测序方法，用了10年，耗资估计US $ 3十亿1，2。然而，自成立以来一点点过去十年，新一代测序（NGS）技术已经使人们有可能在两周内测序整个人类基因组和US $ 1,000。新NGS仪器的成本是允许日益增长的测序数据采集的速度令人难以置信的效率，与急剧下降一起，以难以想象的方式彻底改变现代生物学的基因组测序项目正在迅速成为家常便饭。此外，这些发展已镀锌在许多其他领域，例如通过RNA测序（RNA-SEQ），的基因组范围的表观遗传修饰的研究中，DNA-蛋白质相互作用的基因表达分析的进步，并筛选在人类宿主微生物多样性。 NGS-基于RNA的硒●在特定使得有可能鉴定和地图转录全面与准确度和灵敏度，并且已取代微阵列技术作为选择的一种绘制表达图谱的方法。虽然微阵列技术已经被广泛使用时，它通过其与已知基因组信息预先存在的阵列，以及其它的缺点的依赖的限制，诸如交叉杂交，并且能够可靠地计量的表达的变化限制范围。 RNA-SEQ，在另一方面，可用于检测已知和未知的转录而产生低的背景噪声，由于其明确的DNA映射性质。 RNA-Seq的，加上通过模式生物如酵母提供了众多的遗传工具，蝇，虫，鱼和小鼠，曾担任许多重要生物医学近期发现的基础。然而，显著挑战依然存在，使以更广泛的科学界NGS无法访问，包括存储的局限性，加工，最重要的是，男<html>大量的测序数据的eaningful生物信息学分析。 在测序技术和指数数据积累的快速发展创造了计算平台，将允许研究人员访问，分析和理解这些信息的巨大需求。早期的系统主要依赖于计算机编程知识，反之，基因组浏览器，比如NCBI，允许非程序员访问和可视化数据不允许复杂的分析。基于Web的，开放的接入平台，银河（ <a href="https://galaxyproject.org/" target="_blank">https://galaxyproject.org/</a> ），填补了这一空白，并证明是一个有价值的管道，使研究人员能够处理NGS数据并执行的频谱简单到复杂生物信息学分析。银河初步建立，并保持，由安东Nekrutenko（宾夕法尼亚州立大学）和詹姆斯·泰勒的实验室（约翰霍普金斯大学）F"&gt; 3。银河提供广泛的计算任务使其成为一个‘一站式’为无数生物信息学的需要，包括所有参与的RNA测序研究的步骤。Itallows用户无论是在其服务器或执行数据处理在当地自己的机器上，数据和工作流可以被复制和共享。在线教程，帮助部分和wiki页面 （ <a href="https://wiki.galaxyproject.org/Support" target="_blank">https://wiki.galaxyproject.org/Support</a> ）专用于银河项目提供持续的支持。但是，对于初次使用的用户，尤其是那些没有生物信息学培训，该管道可以出现艰巨，自主学习和熟悉的过程可能会非常耗时。此外，生物系统研究，实验和方法的具体使用，冲击在几个步骤的分析决策，而这些可能很难没有指令导航。 整体RN<html> A-SEQ银河工作流包括数据上传和质量检查，随后使用Tuxedo的套件4，5，6，7，8，9，这是用于RNA测序数据分析10的不同阶段所需的各种工具的集体分析， 11，12，13，14。典型的RNA测序实验由实验部分（样品制备，分离mRNA和cDNA文库制备）中，并NGS生物信息学分析数据。这些部分，以及涉及在银河管道中的步骤的概述，示于图1。 3fig1.jpg" /&gt; 图1:一个RNA测序工作流程的概述。参与的RNA测序实验，以比较两个蠕虫菌株（A和B，橙色和绿色线和箭头，分别地）的基因表达概况的实验和计算步骤图示。银河使用的不同的模块示于盒用在我们的协议以红色表示相应的步骤。各种操作的输出被写在灰色与以蓝色显示的文件格式。 <a href="http://ecsource.jove.com/files/ftp_upload/55473/55473fig1large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> 在炫套房的第一个工具是一个名为" 高顶礼帽 "的比对程序。它分解的NGS输入读取成较小的片段，然后将它们映射到参考基因组。这种两步处理确保读取跨越内含子区，其比对可以以其他方式二srupted或错过入账和映射。这增加了覆盖范围并促进新的剪接点的鉴定。 顶帽输出被报告为两个文件，一个文件BED（具有约剪接点，其包括基因组位置信息）和一个文件BAM（具有每个读映射的详细信息）。接着，BAM文件针对参照基因组对齐来估计使用于所谓的" 袖扣" Tuxedo的套件随后工具每个样品内的单个转录物的丰度。通过扫描对准来报告全长转录物的片段或"transfrags"跨越所有在为每一个基因的输入数据可能的剪接变体袖扣功能。在此基础上，它会产生一个对于每个样品被测序（每个基因产生的每一个基因的所有转录的组件）"转录"。然后，这些袖扣组件崩溃或再一起合并在一起ference基因组以产生用于使用下一个工具，"Cuffmerge"下游差分分析的单个注释文件。最后，由每个样品的顶帽的输出进行比较，以最终Cuffmerge输出文件（ 图1） 的样品之间的"Cuffdiff"工具措施的差异基因表达。 袖扣使用FPKM / RPKM（片段/读取每百万映射成绩单的每千碱基读取）值报告成绩单丰度。这些值反映原始NGS数据的深度归一化和基因长度（基因具有不同的长度，所以计数必须被归一化了的基因，以比较电平的长度（平均数目从对齐到参考基因组中的样本读出）基因之间）。 FPKM和RPKM基本上是相同的与RPKM被用于单端RNA测序，每一个读出对应于一个单一片段，而，FPKM用于配对末端RNA测序，因为它占的事实，两次读取可以对应于相同的片段。最终，这些分析的结果是所测试的条件和/或株之间差异表达的基因的列表。 一旦成功银河运行完成并产生"基因名单"，下一个合乎逻辑的步骤需要更多的生物信息学分析，从数据集推断出有意义的知识。许多软件包应运而生，以满足这方面的需求，其中包括公开可用的基于网络的计算包，如DAVID 15（用于注释，可视化和集成发现数据库）。 DAVID利于通过比较基因上传列表，其集成的生物知识库和揭示与基因列表相关的生物注释分配生物学意义，从高通量研究大基因列表。其次是富集分析， 即测试IDEntify如果任何生物过程或基因类是在以统计学显著方式基因列表（一个或多个）过表达。因为一个广泛的，集成的知识基础和强大的分析算法，使研究人员能够检测富含内生物主题的组合，已成为一个流行的选择基因组衍生的"基因列表" 10，16。其它优点包括其处理的任何测序平台和高度友好的用户界面创建基因列表的能力。 所述线虫是一种遗传模型系统中，公知为它的许多优点，例如尺寸小，透明体，简单的身体计划，易于培养的和巨大的顺从的遗传和分子清扫。蠕虫有一个小的，简单的和注释良好的基因组，其包括高达40％保守的基因与已知的人类同系物17。事实上， 线虫是第一个后生动物，其基因组被完全测序18，并且其中RNA测序被用于映射生物体的转录19，20中的第一物种之一。早期的蠕虫的研究涉及的实验用不同的方法进行高通量RNA捕获，文库制备和测序及生物信息学管道是该技术21，22的发展作出了贡献。近年来，在蠕虫基于RNA-Seq的，实验已经司空见惯。但是，传统的蠕虫生物学家通过RNA-Seq的数据的计算分析所带来的挑战仍然是技术的更大和更好地利用的一个主要障碍。 在本文中，我们描述了使用Galaxy平台分析来自秀丽隐杆线虫中产生高通量的RNA测序数据的协议。对于许多第一次和小SCA勒用户来说，最具有成本效益的和直接的方式进行的RNA测序实验是在实验室中分离RNA，并利用商用（或内部）NGS设施用于制备测序的cDNA文库和NGS本身。因此，我们已首次详细涉及隔离的步骤，C.量化和质量评估线虫 RNA样品用于RNA测序。接下来，我们为使用Galaxy接口，用于NGS数据的分析中，有用于测序后质量控制检查，随后对准，装配，和基因表达的定量差试验开始提供一步一步的指示。此外，我们已包括方向审议银河使用DAVID生物富集研究产生的基因列表。由于工作流中的最后的步骤中，我们上传到公共服务器，如序列读数存档（SRA）在NCBI（RNA-SEQ数据提供指令<a href="http://www.ncbi.nlm.nih.gov/sra" target="_blank">的http://瓦特</a>ww.ncbi.nlm.nih.gov/sra），使其自由科学界访问。总体而言，我们预计，本文将蠕虫生物学家开展运行小样本首次RNA-Seq的实验以及频繁的用户提供全面的，充分的信息。

<table><tbody><tr><td>RNase spray&amp;nbsp;</td><td>Fisher Scientific</td><td>21-402-178</td><td></td></tr><tr><td>Trizol&amp;nbsp;</td><td>Ambion</td><td>15596026</td><td></td></tr><tr><td>Sonicator</td><td>Sonics Vibra Cell&amp;nbsp;</td><td>VCX130</td><td></td></tr><tr><td>Centrifuge&amp;nbsp;</td><td>Eppendorf</td><td>5415C</td><td></td></tr><tr><td>chloroform&amp;nbsp;</td><td>Sigma Aldrich</td><td>288306</td><td></td></tr><tr><td>2-propanol&amp;nbsp;</td><td>Fisher Scientific</td><td>A416P-4</td><td></td></tr><tr><td>Ethanol</td><td>Decon Labs</td><td>2705HC</td><td></td></tr><tr><td>RNase-free water&amp;nbsp;</td><td>Fisher Scientific</td><td>BP561-1</td><td></td></tr><tr><td>Bioanalyzer&amp;nbsp;</td><td>Agilent</td><td>G2940CA</td><td></td></tr><tr><td>Mac/PC</td><td></td><td></td><td></td></tr></tbody></table>

transcriptomic analysis of c. elegans rna sequencing data through the tuxedo suite on the galaxy project

新一代测序（NGS）技术已经彻底改变了生物学研究的性质。在这些中，RNA测序（RNA-SEQ）已经成为用于基因表达分析和转录的映射的有力工具。然而，处理RNA-Seq的数据集需要复杂计算的专业知识和带来的生物学研究人员固有的挑战。这个瓶颈已经缓解由开放接入银河项目，使用户无需生物信息学技术分析RNA-Seq的数据，和注释，可视化和集成发现（DAVID）的数据库，基因本体论（GO）项的分析工具，帮助从大的数据集获得生物学意​​义。但是，对于初次使用者和生物信息学爱好者，自学习和熟悉这些平台可以是耗时且艰巨。我们描述一个简单的工作流程，这将有助于线虫研究人员分离出病毒RNA，进行了RNA-Seq的实验并分析利用银河DAVID平台的数据。这个协议提供了使用各种银河模块在每个步骤访问原始NGS数据，质量控制检查，对准和差异基因表达分析，指导与参数的用户生成可筛选的富集的基因列表逐步指令基因的类或使用DAVID生物过程。总体而言，我们预计，本文将提供信息，以秀丽隐杆线虫的研究人员正在进行运行的小样本首次RNA-Seq的实验以及频繁的用户。

在秀丽隐杆线虫 ，消去生殖系干细胞（GSC中）延长寿命，提高的应力复原力，和提升体脂肪24,28。 GSC中的损失，或者通过激光烧蚀或通过突变如GLP-1引起，导致寿命延长通过转录的网络因子29活化。一个这样的因素，TCER-1，编码人转录延伸和剪接因子，TCERG1 30的蜗杆同源物...

Watch this Scientific Journal Video about Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project at JoVE.com

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

银河和大卫已经成为流行的工具，让没有生物信息学培训调查分析和解释RNA-Seq的数据。我们描述了一种协议，用于秀丽隐杆线虫的研究人员进行RNA测序实验，访问和使用银河处理数据集，并获得从使用DAVID的基因列表有意义的生物信息。

的转录分析<em&gt;ç</em&gt;。<em&gt;线虫</em&gt; RNA测序数据通过炫套房的银河项目

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

transcriptomic-analysis-c-elegans-rna-sequencing-data-through-tuxedo

Research

JoVE Journal

Genetics

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

17.3K 次观看.  University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh. 银河和大卫已经成为流行的工具，让没有生物信息学培训调查分析和解释RNA-Seq的数据。我们描述了一种协议，用于秀丽隐杆线虫的研究人员进行RNA测序实验，访问和使用银河处理数据集，并获得从使用DAVID的基因列表有意义的生物信息。 

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

Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response

Complex changes in gene expression typically mediate a large portion of a cellular response. Each gene may change expression with unique kinetics as the gene is regulated by the particular timing of one of many stimuli, signaling pathways or secondary effects. In order to capture the entire gene expression response to hypoxia in the yeast S. cerevisiae, RNA-seq analysis was used to monitor the mRNA levels of all genes at specific times after exposure to hypoxia. Hypoxia was established by growing cells in ~100% N2 gas. Importantly, unlike other hypoxic studies, ergosterol and unsaturated fatty acids were not added to the media because these metabolites affect gene expression. Time points were chosen in the range of 0 - 4 h after hypoxia because that period captures the major changes in gene expression. At each time point, mid-log hypoxic cells were quickly filtered and frozen, limiting exposure to O2 and concomitant changes in gene expression. Total RNA was extracted from cells and used to enrich for mRNA, which was then converted to cDNA. From this cDNA, multiplex libraries were created and eight or more samples were sequenced in one lane of a next-generation sequencer. A post-sequencing pipeline is described, which includes quality base trimming, read mapping and determining the number of reads per gene. DESeq2 within the R statistical environment was used to identify genes that change significantly at any one of the hypoxic time points. Analysis of three biological replicates revealed high reproducibility, genes of differing kinetics and a large number of expected O2-regulated genes. These methods can be used to study how the cells of various organisms respond to hypoxia over time and adapted to study gene expression during other cellular responses.

Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response

Here, we present a protocol using RNA-seq to monitor mRNA levels over time during the hypoxic response of S. cerevisiae cells. This method can be adapted to analyze gene expression during any cellular response.

在酵母S.酵母缺氧反应期间, 测量一段时间内的 mRNA 水平

Complex changes in gene expression typically mediate a large portion of a cellular response. Each gene may change expression with unique kinetics as the ...

科研

遗传学

Defining Gene Functions in Tumorigenesis by Ex vivo Ablation of Floxed Alleles in Malignant Peripheral Nerve Sheath Tumor Cells

The development of new drugs that precisely target key proteins in human cancers is fundamentally altering cancer therapeutics. However, before these drugs can be used, their target proteins must be validated as therapeutic targets in specific cancer types. This validation is often performed by knocking out the gene encoding the candidate therapeutic target in a genetically engineered mouse (GEM) model of cancer and determining what effect this has on tumor growth. Unfortunately, technical issues such as embryonic lethality in conventional knockouts and mosaicism in conditional knockouts often limit this approach. To overcome these limitations, an approach to ablating a floxed embryonic lethal gene of interest in short-term cultures of malignant peripheral nerve sheath tumors (MPNSTs) generated in a GEM model was developed.
This paper describes how to establish a mouse model with the appropriate genotype, derive short-term tumor cultures from these animals, and then ablate the floxed embryonic lethal gene using an adenoviral vector that expresses Cre recombinase and enhanced green fluorescent protein (eGFP). Purification of cells transduced with adenovirus using fluorescence-activated cell sorting (FACS) and the quantification of the effects that gene ablation exerts on cellular proliferation, viability, the transcriptome, and orthotopic allograft growth is then detailed. These methodologies provide an effective and generalizable approach to identifying and validating therapeutic targets in vitro and in vivo. These approaches also provide a renewable source of low-passage tumor-derived cells with reduced in vitro growth artifacts. This allows the biological role of the targeted gene to be studied in diverse biologic processes such as migration, invasion, metastasis, and intercellular communication mediated by the secretome.

Defining Gene Functions in Tumorigenesis by Ex vivo Ablation of Floxed Alleles in Malignant Peripheral Nerve Sheath Tumor Cells

Here, we present a protocol for performing gene knockouts that are embryonic lethal in vivo in genetically engineered mouse model-derived tumors and then assessing the effect that the knockout has on tumor growth, proliferation, survival, migration, invasion, and the transcriptome in vitro and in vivo.

通过恶性周围神经鞘肿瘤细胞中絮状等位基因的 离体 消融来定义肿瘤发生的基因功能

The development of new drugs that precisely target key proteins in human cancers is fundamentally altering cancer therapeutics. However, before these ...

癌症研究

秀丽隐杆线虫的表观遗传遗传和 ChIP

Analysis of Transgenerational Epigenetic Inheritance in C. elegans Using a Fluorescent Reporter and Chromatin Immunoprecipitation (ChIP)

Transgenerational epigenetic inheritance (TEI) allows the transmission of information through the germline without changing the genome sequence, through factors such as non-coding RNAs and chromatin modifications. The phenomenon of RNA interference (RNAi) inheritance in the nematode Caenorhabditis elegans is an effective model to investigate TEI that takes advantage of this model organism's short life cycle, self-propagation, and transparency. In RNAi inheritance, exposure of animals to RNAi leads to gene silencing and altered chromatin signatures at the target locus that persist for multiple generations in the absence of the initial trigger. This protocol describes the analysis of RNAi inheritance in C. elegans using a germline-expressed nuclear green fluorescent protein (GFP) reporter. Reporter silencing is initiated by feeding the animals bacteria expressing double-stranded RNA targeting GFP. At each generation, animals are passaged to maintain synchronized development, and reporter gene silencing is determined by microscopy. At select generations, populations are collected and processed for chromatin immunoprecipitation (ChIP)-quantitative polymerase chain reaction (qPCR) to measure histone modification enrichment at the GFP reporter locus. This protocol for studying RNAi inheritance can be easily modified and combined with other analyses to further investigate TEI factors in small RNA and chromatin pathways.

作者聚焦:秀丽隐杆线虫的 RNAi 遗传和 ChIP 

This protocol describes an RNA interference and ChIP assay to study the epigenetic inheritance of RNAi-induced silencing and associated chromatin modifications in C. elegans.

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析 秀丽隐杆线虫 的跨代表观遗传

Transgenerational epigenetic inheritance (TEI) allows the transmission of information through the germline without changing the genome sequence, through ...

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

In ovo electroporation of the chick neural tube is a fast and inexpensive method for identification of gene function during neural development. Genome wide analysis of differentially expressed transcripts after such an experimental manipulation has the potential to uncover an almost complete picture of the downstream effects caused by the transfected construct. This work describes a simple method for comparing transcriptomes from samples of transfected embryonic spinal cords comprising all steps between electroporation and identification of differentially expressed transcripts. The first stage consists of guidelines for electroporation and instructions for dissection of transfected spinal cord halves from HH23 embryos in ribonuclease-free environment and extraction of high-quality RNA samples suitable for transcriptome sequencing. The next stage is that of bioinformatic analysis with general guidelines for filtering and comparison of RNA-Seq datasets in the Galaxy public server, which eliminates the need of a local computational structure for small to medium scale experiments. The representative results show that the dissection methods generate high quality RNA samples and that the transcriptomes obtained from two control samples are essentially the same, an important requirement for detection of differential expression genes in experimental samples. Furthermore, one example is provided where experimental overexpression of a DNA construct can be visually verified after comparison with control samples. The application of this method may be a powerful tool to facilitate new discoveries on the function of neural factors involved in spinal cord early development.

This video shows the basic steps for performing whole transcriptome analysis on dissected chick embryonic spinal cord samples after transfection with in ovo electroporation.

对基因差异表达的RNA序列中电穿孔鸡胚脊髓分析

In ovo electroporation of the chick neural tube is a fast and inexpensive method for identification of gene function during neural development. Genome ...

神经科学

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Synapses are composed of a presynaptic active zone in the signaling cell and a postsynaptic terminal in the target cell. In the case of chemical synapses, messages are carried by neurotransmitters released from presynaptic terminals and received by receptors on postsynaptic cells. Our previous research in Caenorhabditis elegans has shown that VSM-1 negatively regulates exocytosis. Additionally, analysis of synapses in vsm-1 mutants showed that animals lacking a fully functional VSM-1 have increased synaptic connectivity. Based on these preliminary findings, we hypothesized that C. elegans VSM-1 may play a crucial role in synaptogenesis. To test this hypothesis, double-labeled microarray analysis was performed, and gene expression profiles were determined. First, total RNA was isolated, reversely transcribed to cDNA, and hybridized to the DNA microarrays. Then, in-silico analysis of fluorescent probe hybridization revealed significant induction of many genes coding for members of the major sperm protein family (MSP) in mutants with enhanced synaptogenesis. MSPs are the major component of sperm in C. elegans and appear to signal nematode oocyte maturation and ovulation . In fruit flies, Chai and colleagues 1 demonstrated that MSP-like molecules regulate presynaptic bouton number and size at the neuromuscular junction. Moreover, analysis performed by Tsuda and coworkers 2 suggested that MSPs may act as ligands for Eph receptors and trigger receptor tyrosine kinase signaling cascades. Lastly, real time PCR analysis corroborated that the gene coding for MSP-32 is induced in vsm-1(ok1468) mutants. Taken together, research performed by our laboratory has shown that vsm-1 mutants have a significant increase in synaptic density, which could be mediated by MSP-32 signaling.

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Microarray analysis was conducted to determine genetic expression profiles in C. elegans, and real-time PCR was used to validate and quantify microarray data.

确定基因表达概况 C。线虫使用微阵列和实时PCR

Synapses are composed of a presynaptic active zone in the signaling cell and a postsynaptic terminal in the target cell. In the case of chemical synapses, ...

生物学

Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans

RNA interference is a powerful method to understand gene function, especially when conducted at a whole-genome scale and in a quantitative context. In C. elegans, gene function can be knocked down simply and efficiently by feeding worms with bacteria expressing a dsRNA corresponding to a specific gene 1. While the creation of libraries of RNAi clones covering most of the C. elegans genome 2,3 opened the way for true functional genomic studies (see for example 4-7), most established methods are laborious. Moy and colleagues have developed semi-automated protocols that facilitate genome-wide screens 8. The approach relies on microscopic imaging and image analysis. 
	Here we describe an alternative protocol for a high-throughput genome-wide screen, based on robotic handling of bacterial RNAi clones, quantitative analysis using the COPAS Biosort (Union Biometrica (UBI)), and an integrated software: the MBioLIMS (Laboratory Information Management System from Modul-Bio) a technology that provides increased throughput for data management and sample tracking. The method allows screens to be conducted on solid medium plates. This is particularly important for some studies, such as those addressing host-pathogen interactions in C. elegans, since certain microbes do not efficiently infect worms in liquid culture.
	We show how the method can be used to quantify the importance of genes in anti-fungal innate immunity in C. elegans. In this case, the approach relies on the use of a transgenic strain carrying an epidermal infection-inducible fluorescent reporter gene, with GFP under the control of the promoter of the antimicrobial peptide gene nlp 29 and a red fluorescent reporter that is expressed constitutively in the epidermis. The latter provides an internal control for the functional integrity of the epidermis and nonspecific transgene silencing9. When control worms are infected by the fungus they fluoresce green. Knocking down by RNAi a gene required for nlp 29 expression results in diminished fluorescence after infection. Currently, this protocol allows more than 3,000 RNAi clones to be tested and analyzed per week, opening the possibility of screening the entire genome in less than 2 months.

Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans

We describe a protocol using C. elegans and RNAi feeding libraries that allows automated measurement of multiple parameters such as fluorescence, size and opacity of individual worms in a population. We give one example of a screen to identify genes involved in anti-fungal innate immunity in C. elegans.

定量和自动化高通量的全基因组RNAi屏幕 C。线虫</em

RNA interference is a powerful method to understand gene function, especially when conducted at a whole-genome scale and in a quantitative context. In C. ...

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as leukemia and lymphoma. Elucidating the mechanisms controlling HSCs self-renewal and differentiation is important for application of HSCs for research and clinical uses. However, it is not possible to obtain large quantity of HSCs due to their inability to proliferate in vitro. To overcome this hurdle, we used a mouse bone marrow derived cell line, the EML (Erythroid, Myeloid, and Lymphocytic) cell line, as a model system for this study.
RNA-sequencing (RNA-Seq) has been increasingly used to replace microarray for gene expression studies. We report here a detailed method of using RNA-Seq technology to investigate the potential key factors in regulation of EML cell self-renewal and differentiation. The protocol provided in this paper is divided into three parts. The first part explains how to culture EML cells and separate Lin-CD34+ and Lin-CD34- cells. The second part of the protocol offers detailed procedures for total RNA preparation and the subsequent library construction for high-throughput sequencing. The last part describes the method for RNA-Seq data analysis and explains how to use the data to identify differentially expressed transcription factors between Lin-CD34+ and Lin-CD34- cells. The most significantly differentially expressed transcription factors were identified to be the potential key regulators controlling EML cell self-renewal and differentiation. In the discussion section of this paper, we highlight the key steps for successful performance of this experiment.
In summary, this paper offers a method of using RNA-Seq technology to identify potential regulators of self-renewal and differentiation in EML cells. The key factors identified are subjected to downstream functional analysis in vitro and in vivo.

RNA-sequencing and bioinformatics analyses were used to identify significantly and differentially expressed transcription factors in Lin-CD34+ and Lin-CD34- subpopulations of mouse EMLcells. These transcription factors might play important roles in determining the switch between self-renewing Lin-CD34+ and partially differentiated Lin-CD34- cells.

在EML造血前体细胞调节自我更新和分化的关键因素，通过RNA测序分析鉴定

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as ...

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 - 100 million sequencing reads and can include multiple RNA products such as mRNA and noncoding RNAs. We demonstrate how targeted RNAseq (capture) permits a focused study on selected RNA products using a desktop sequencer. RNAseq capture can characterize unannotated, low, or transiently expressed transcripts that may otherwise be missed using traditional RNAseq methods. Here we describe the extraction of RNA from cell lines, ribosomal RNA depletion, cDNA synthesis, preparation of barcoded libraries, hybridization and capture of targeted transcripts and multiplex sequencing on a desktop sequencer. We also outline the computational analysis pipeline, which includes quality control assessment, alignment, fusion detection, gene expression quantification and identification of single nucleotide variants. This assay allows for targeted transcript sequencing to characterize gene expression, gene fusions, and mutations.

We describe a targeted RNA sequencing-based method that includes preparation of indexed cDNA libraries, hybridization and capture with custom probes and data analysis to interrogate selected transcripts for gene expression, mutations, and gene fusions. Targeted RNAseq permits cost-effective, rapid evaluation of selected transcripts on a desktop sequencer.

有针对性的RNA测序分析表征基因表达和基因组改变

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding ...

的转录分析

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此视频中的章节

在酵母S.酵母缺氧反应期间, 测量一段时间内的 mRNA 水平

通过恶性周围神经鞘肿瘤细胞中絮状等位基因的离体消融来定义肿瘤发生的基因功能

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析秀丽隐杆线虫的跨代表观遗传

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析秀丽隐杆线虫的跨代表观遗传

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析秀丽隐杆线虫的跨代表观遗传

对基因差异表达的RNA序列中电穿孔鸡胚脊髓分析

确定基因表达概况 C。线虫使用微阵列和实时PCR

定量和自动化高通量的全基因组RNAi屏幕 C。线虫

在EML造血前体细胞调节自我更新和分化的关键因素，通过RNA测序分析鉴定

有针对性的RNA测序分析表征基因表达和基因组改变

的转录分析

摘要

探索更多视频

此视频中的章节

在酵母S.酵母缺氧反应期间, 测量一段时间内的 mRNA 水平

通过恶性周围神经鞘肿瘤细胞中絮状等位基因的 离体 消融来定义肿瘤发生的基因功能

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析 秀丽隐杆线虫 的跨代表观遗传

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析 秀丽隐杆线虫 的跨代表观遗传

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析 秀丽隐杆线虫 的跨代表观遗传

对基因差异表达的RNA序列中电穿孔鸡胚脊髓分析

确定基因表达概况 C。线虫使用微阵列和实时PCR

定量和自动化高通量的全基因组RNAi屏幕 C。线虫

在EML造血前体细胞调节自我更新和分化的关键因素，通过RNA测序分析鉴定

有针对性的RNA测序分析表征基因表达和基因组改变

通过恶性周围神经鞘肿瘤细胞中絮状等位基因的离体消融来定义肿瘤发生的基因功能

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析秀丽隐杆线虫的跨代表观遗传

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析秀丽隐杆线虫的跨代表观遗传

基于荧光报告基因和染色质免疫沉淀法（ChIP）分析秀丽隐杆线虫的跨代表观遗传