Name: de novo identification of actively translated open reading frames with ribosome profiling data
Uploaded: 2022-02-18T13:45:00
Description: Watch this Scientific Journal Video about De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data at JoVE.com

作者要感谢西安交通大学HPCC平台提供的计算资源的支持。Z.X.衷心感谢西安交通大学青年顶尖人才支持计划。

1. 环境设置和 RiboCode 安装
<ol><li>打开一个 Linux 终端窗口并创建一个 conda 环境： conda create -n RiboCode python=3.8
</li>
	<li>切换到创建的环境并安装 RiboCode 和依赖项： 康达激活核糖代码 conda install -c bioconda ribocode ribominer sra-tools fastx_toolkit cutadapt bowtie star samtools
</li>
</ol>2. 数据准备
<ol><li>获取基因组参考文件。<ol>
<li>有关参考序列，请转...

<ol>
	<li>Eisenberg, A. R., 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=Translation+Initiation+Site+Profiling+Reveals+Widespread+Synthesis+of+Non-AUG-Initiated+Protein+Isoforms+in+Yeast.">Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast.</a> Cell Systems. 11 (2), 145-160 (2020).</li><li>Spealman, P., 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=Conserved+non-AUG+uORFs+revealed+by+a+novel+regression+analysis+of+ribosome+profiling+data.">Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data.</a> Genome Research. 28 (2), 214-222 (2018).</li><li>Ingolia, N. T., Lareau, L. F., Weissman, J. 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T., 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=Ribosome+profiling+reveals+pervasive+translation+outside+of+annotated+protein-coding+genes.">Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes.</a> Cell Reports. 8 (5), 1365-1379 (2014).</li><li>Chew, G. L., Pauli, A., Schier, A. 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C., Ho, L., Tian, J., Reversade, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ELABELA:+a+hormone+essential+for+heart+development+signals+via+the+apelin+receptor.">ELABELA: a hormone essential for heart development signals via the apelin receptor.</a> Developmental Cell. 27 (6), 672-680 (2013).</li><li>Pauli, 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=Toddler:+an+embryonic+signal+that+promotes+cell+movement+via+Apelin+receptors.">Toddler: an embryonic signal that promotes cell movement via Apelin receptors.</a> Science. 343 (6172), 1248636 (2014).</li><li>Stark, 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=Discovery+of+functional+elements+in+12+Drosophila+genomes+using+evolutionary+signatures.">Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.</a> Nature. 450 (7167), 219-232 (2007).</li><li>Lin, M. F., Jungreis, I., Kellis, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PhyloCSF:+a+comparative+genomics+method+to+distinguish+protein+coding+and+non-coding+regions.">PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.</a> Bioinformatics. 27 (13), 275-282 (2011).</li><li>Slavoff, 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=Peptidomic+discovery+of+short+open+reading+frame-encoded+peptides+in+human+cells.">Peptidomic discovery of short open reading frame-encoded peptides in human cells.</a> Nature Chemical Biology. 9 (1), 59-64 (2013).</li><li>Schwaid, A. G., 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=Chemoproteomic+discovery+of+cysteine-containing+human+short+open+reading+frames.">Chemoproteomic discovery of cysteine-containing human short open reading frames.</a> Journal of the American Chemical Society. 135 (45), 16750-16753 (2013).</li><li>Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M., Weissman, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-wide+annotation+and+quantitation+of+translation+by+ribosome+profiling.">Genome-wide annotation and quantitation of translation by ribosome profiling.</a> Current Protocols in Molecular Biology. , 1-19 (2013).</li><li>Ingolia, N. T., Ghaemmaghami, S., Newman, J. R., Weissman, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-wide+analysis+in+vivo+of+translation+with+nucleotide+resolution+using+ribosome+profiling.">Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.</a> Science. 324 (5924), 218-223 (2009).</li><li>Xiao, Z., 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=De+novo+annotation+and+characterization+of+the+translatome+with+ribosome+profiling+data.">De novo annotation and characterization of the translatome with ribosome profiling data.</a> Nucleic Acids Research. 46 (10), 61 (2018).</li><li>Lin, Y., 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=eIF3+Associates+with+80S+Ribosomes+to+Promote+Translation+Elongation,+Mitochondrial+Homeostasis,+and+Muscle+Health.">eIF3 Associates with 80S Ribosomes to Promote Translation Elongation, Mitochondrial Homeostasis, and Muscle Health.</a> Molecular Cell. 79 (4), 575-587 (2020).</li><li>. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format Available from: <a target="_blank" href="https://agat.readthedocs.io/en/latest/gff_to_gtf.html">https://agat.readthedocs.io/en/latest/gff_to_gtf.html</a> (2020)</li><li>. Gene Expression Omnibus Available from: <a target="_blank" href="https://www.ncbi.nim.nih.gov/geo">https://www.ncbi.nim.nih.gov/geo</a> (2002)</li><li>Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M., Weissman, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ribosome+profiling+strategy+for+monitoring+translation+in+vivo+by+deep+sequencing+of+ribosome-protected+mRNA+fragments.">The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.</a> Nature Protocols. 7 (8), 1534-1550 (2012).</li><li>. STAR manual Available from: <a target="_blank" href="https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf">https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf</a> (2022)</li><li>. The genetic codes Available from: <a target="_blank" href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi</a> (2019)</li><li>. RiboMiner Available from: <a target="_blank" href="https://github.com/xryanglab/RiboMiner">https://github.com/xryanglab/RiboMiner</a> (2020)</li><li>Ingolia, N. T., Hussmann, J. A., Weissman, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ribosome+profiling:+global+views+of+translation.">Ribosome profiling: global views of translation.</a> Cold Spring Harbor Perspectives in Biology. 11 (5), 032698 (2018).</li><li>Lee, S., 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=Global+mapping+of+translation+initiation+sites+in+mammalian+cells+at+single-nucleotide+resolution.">Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.</a> Proceedings of the National Academy of Sciences of the United States of America. 109 (37), 2424-2432 (2012).</li><li>Gao, X., 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=Quantitative+profiling+of+initiating+ribosomes+in+vivo.">Quantitative profiling of initiating ribosomes in vivo.</a> Nature Methods. 12 (2), 147-153 (2015).</li><li>Spealman, P., Naik, A., McManus, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=uORF-seqr:+A+Machine+Learning-Based+approach+to+the+identification+of+upstream+open+reading+frames+in+yeast.">uORF-seqr: A Machine Learning-Based approach to the identification of upstream open reading frames in yeast.</a> Methods in Molecular Biol. 2252, 313-329 (2021).</li><li>. 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核糖体分析为在基因组尺度上研究核糖体在细胞中的作用提供了前所未有的机会。精确破译核糖体分析数据携带的信息可以深入了解基因或转录本的哪些区域正在积极翻译。此分步协议提供了有关如何使用 RiboCode 详细分析核糖体分析数据的指导，包括软件包安装、数据准备、命令执行、结果说明和数据可视化。RiboCode的分析结果表明，翻译是普遍存在的，并且发生在编码基因的未注释ORF和许多先?...

最近，越来越多的研究表明，从编码基因的ORF和先前注释的基因翻译的肽被广泛生产为非编码基因，例如长非编码RNA（lncRNA）1，2，3，4，5，6，7，8。这些翻译的ORF由细胞调节或诱导，以响应环境变化，压力和细胞分化1，8，9，10，11，12，13。一些ORF的转化产物已被证明在发育和生理学中的各种生物过程中起着重要的调节作用。例如，Chng等人14发现了一种名为Elabela（Ela，也称为Apela / Ende / Toddler）的肽激素，它对心血管发育至关重要。Pauli等人认为Ela还充当有丝分裂原，促进早期鱼胚胎中的细胞迁移15。Magny等人报道了两种少于30个氨基酸的微肽调节钙转运并影响果蝇心脏的正常肌肉收缩10。
目前尚不清楚基因组编码了多少这样的肽，以及它们是否具有生物学相关性。因此，系统地识别这些潜在编码的ORF是非常可取的。然而，使用进化守恒16，17和质谱18，19等传统方法直接确定这些ORF（即蛋白质或肽）的产物具有挑战性，因为这两种方法的检测效率都取决于所产生的蛋白质或肽的长度，丰度和氨基酸组成。核糖体分析是一种在核苷酸分辨率下鉴定mRNA上核糖体占用的技术，它的出现为评估不同转录本的编码潜力提供了一种精确的方法3，20，21，无论它们的长度和组成如何。使用核糖体分析鉴定主动翻译ORF的一个重要且常用的特征是核糖体从起始密码子到停止密码子在mRNA上的足迹的三核苷酸（3-nt）周期性。然而，核糖体分析数据通常存在几个问题，包括沿ORF的低和稀疏测序读数，高测序噪声和核糖体RNA（rRNA）污染。因此，这些数据产生的扭曲和模糊信号削弱了核糖体在mRNA上足迹的3-nt周期模式，最终使得高置信翻译ORFs的鉴定变得困难。
一个名为“RiboCode”的软件包采用了改进的Wilcoxon签名秩测试和P值积分策略，以检查ORF是否比帧外RPF具有更多的帧内核糖体保护片段（RPM）22。它被证明对于模拟和真实核糖体分析数据中翻译组的 从头 注释是高效，灵敏和准确的。在这里，我们描述了如何使用该工具从先前研究生成的原始核糖体分析测序数据集中检测潜在的转化ORF23。这些数据集用于通过比较MCF-10A细胞的核糖体占用谱来探索EIF3亚基“E”（EIF3E）在翻译中的功能，这些细胞转染对照（si-Ctrl）和 EIF3E （si-eIF3e）小干扰RNA（siRNA）。通过将RiboCode应用于这些示例数据集，我们检测到5，633个可能编码小肽或蛋白质的新型ORF。这些ORF根据其相对于编码区域的位置分为各种类型，包括上游ORF（uORFs），下游ORF（dORFs），重叠ORF，来自新型蛋白质编码基因（新型PCG）的ORF以及来自新型非蛋白编码基因（新型NonPCGs）的ORF。与对照细胞相比，EIF3E缺陷细胞中uORFs上的RPF读数密度显着增加，这可能至少部分是由主动翻译核糖体的富集引起的。EIF3E缺陷细胞第25~ 75个 密码子区域的局部核糖体积累表明早期翻译伸长受阻。该协议还展示了如何可视化所需区域的RPF密度，以检查已识别ORF上核糖体足迹的3-nt周期模式。这些分析证明了RiboCode在识别翻译ORF和研究翻译监管方面的强大作用。

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>A computer/server running Linux</td>
			<td>Any</td>
			<td>-</td>
			<td>-</td>
		</tr>
		<tr>
			<td>Anaconda or Miniconda</td>
			<td>Anaconda</td>
			<td>-</td>
			<td>Anaconda: https://www.anaconda.com; Miniconda:https://docs.conda.io/en/latest/miniconda.html</td>
		</tr>
		<tr>
			<td>R</td>
			<td>R Foundation</td>
			<td>-</td>
			<td>https://www.r-project.org/</td>
		</tr>
		<tr>
			<td>Rstudio</td>
			<td>Rstudio</td>
			<td>-</td>
			<td>https://www.rstudio.com/</td>
		</tr>
	</tbody>
</table>

de novo identification of actively translated open reading frames with ribosome profiling data

识别开放阅读框（ORF），特别是那些编码小肽并在特定生理环境下被积极翻译的阅读框，对于上下文依赖性翻译组的全面注释至关重要。核糖体分析是一种检测RNA上翻译核糖体的结合位置和密度的技术，为快速发现全基因组范围内翻译发生的位置提供了一条途径。然而，在生物信息学中，高效、全面地鉴定用于核糖体分析的转化ORFs并非易事。这里描述的是一个易于使用的包，名为RiboCode，旨在从核糖体分析数据中的失真和模糊信号中搜索任何大小的ORF。本文以我们之前发布的数据集为例，提供了整个RiboCode管道的分步说明，从原始数据的预处理到最终输出结果文件的解释。此外，为了评估注释ORF的平移率，还详细描述了每个ORF上核糖体密度的可视化和定量程序。综上所述，本文是对翻译、小ORF和肽相关研究领域的有用和及时的指导。

将示例核糖体分析数据集存入GEO数据库，加入号为GSE131074。此协议中使用的所有文件和代码均可从补充文件 1-4 获得。通过将RiboCode应用于一组已发表的核糖体分析数据集23，我们确定了在用对照和EIF3E siRNA处理的MCF-10A细胞中主动翻译的新型ORF。为了选择最有可能被翻译核糖体结合的RPF读数，检查了测序读数的长度，并使用映射在已知?...

Watch this Scientific Journal Video about De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data at JoVE.com

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

翻译核糖体将每个密码子的三个核苷酸解码为肽。它们沿着mRNA的运动，通过核糖体分析捕获，产生表现出特征性三重态周期性的足迹。该协议描述了如何使用RiboCode从核糖体分析数据中破译这一突出特征，以识别全转录组水平上主动翻译的开放阅读框。

从头 使用核糖体分析数据识别主动翻译的开放阅读框

Identification of open reading frames (ORFs), especially those encoding small peptides and being actively translated under specific physiological ...

解释核糖体分析实验产生的测序数据对于定量测量核糖体在mRNA上的翻译活性以及研究翻译调控机制至关重要。在该协议中，我们将描述利用核糖体分析数据和RiboCode的计算过程，RiboCode是一种命令行工具，用于在全基因组尺度和单核苷酸分辨率下解码mRNA翻译。这种方法允许搜索来自注释蛋白质编码基因之外的基因组区域的新型肽，并提供量化mRNA翻译速率的机会。首先，打开一个 Linux 终端窗口，然后通过执行命令创建 conda 环境。切换到创建的环境，并通过执行命令安装 RiboCode 和依赖项。要获取参考序列的基因组参考文件，请转到Ensembl网站，然后单击下载，然后单击FTP下载。单击“DNA FASTA”列中的“FASTA”选项，然后选择物种为人类的行，如网站页面上的表格所示。在Ensembl网站页面上，复制文本中提到的链接，然后通过执行命令下载并解压缩终端中的文件。有关参考注释，请右键单击上次打开的网页中列基因集中的 GTF。复制链接，然后使用命令下载。要获取 rRNA 序列，请打开 UCSC 基因组浏览器，然后单击工具，然后在下拉列表中选择表格浏览器。在 UCSC 基因组浏览器页面上，为进化枝指定哺乳动物，为基因组指定人类，为组指定所有表，为表指定 R 掩码，为区域指定基因组。对于过滤器，单击“创建”转到新页面，并将 rep 类设置为匹配 rRNA。单击“提交”，然后将输出格式设置为序列，并将文件名输出为HG38_rRNA。发。最后，单击“获取输出”，然后选择“获取序列”以检索 rRNA 序列。要从序列读取存档中获取核糖体分析数据集，请下载si-eIFe处理组的复制样本，并通过执行命令重命名它们。然后下载对照组的复制样本，并通过执行命令重命名它们。要去除 rRNA 污染，请通过执行命令开始索引 rRNA 参考序列。索引后，将读数与 rRNA 引用对齐，以通过执行命令排除源自 rRNA 的读取。首先通过执行命令创建基因组索引。然后，通过执行命令将无 rRNA 污染的干净读取与创建的引用对齐，然后通过执行命令对准文件进行排序和索引。通过执行命令准备脚本批注。选择特定长度的核糖体保护片段，并通过执行命令来识别它们的P位点位置。编辑每个示例的配置文件并合并它们。然后通过执行命令运行RiboCode。读数长度的频率分布表明，大多数受核糖体保护的片段对应于25至35个核苷酸。通过检查不同长度的核糖体保护片段的P位点位置，通过检查其从五个主端到注释的起始和停止密码子的距离来确定。映射结果表明，10， 394个基因编码带注释的开放阅读框。此外，509和168个基因编码上游和下游开放阅读框，而939个基因编码上游或下游开放阅读框架，与已知的注释开放阅读框架重叠。此外，68个蛋白质编码基因和2，601个非编码基因编码新型开放阅读框。长度分布表明，上游、下游、新颖和重叠的开放阅读框比注释的开放阅读框架短。计算每个开放阅读框的相对核糖体保护片段计数，结果表明，eIF3e缺陷细胞中上游开放阅读框的核糖体密度显着高于对照细胞。元遗传学分析显示，在起始密码子下游的密码子25和75之间停滞了大量核糖体，这表明翻译伸长可能在eIF3e缺陷细胞的早期被阻断。研究了PSMA6上游开放阅读框和基因SENP3-EIF4A1下游开放阅读框架的P位点密度谱，证明了核糖体保护片段的周期模式和密度。检查已知蛋白质编码区域的开始和停止密码子周围的读取位置对于评估每个长度的读取周期性是必要的。RiboCode与另一个命令行工具一起，RiboMiner还可以执行质量控制和多种分析，例如量化和可视化核糖体在预测的开放阅读框上的占用率。该计算工具提供了一种高通量方法，用于在特定生理环境中使用核糖体分析数据识别非规范翻译事件，以及翻译如何响应刺激进行调节。

Research

JoVE Journal

Biology

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

蛋白质智慧：一个工作台<em&gt;硅片</em&gt;<em&gt;从头</em&gt;生物分子设计

The aim of de novo protein design is to find the amino acid sequences that will fold into a desired 3-dimensional structure with improvements in specific ...

科研

生物学

Analysis of Translation Initiation During Stress Conditions by Polysome Profiling

翻译起始的分析在应力条件由多聚核糖体剖析

Precise control of mRNA translation is fundamental for eukaryotic cell homeostasis, particularly in response to physiological and pathological stress. ...

Workflow for High-content, Individual Cell Quantification of Fluorescent Markers from Universal Microscope Data, Supported by Open Source Software

工作流的高含量，荧光标记的万能工具显微镜数据，支持开源软件的单个细胞定量

Advances in understanding the control mechanisms governing the behavior of cells in adherent mammalian tissue culture models are becoming increasingly ...

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

染色质免疫沉淀拟南芥蛋白-DNA相互作用的鉴定<em&gt;在体内</em

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and ...

An Easy Method for Plant Polysome Profiling

植物多聚核糖体剖面的简单方法

Translation of mRNA to protein is a fundamental and highly regulated biological process. Polysome profiling is considered as a gold standard for the ...

Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper

与VirusMapper超分辨率显微镜开源单粒子分析

Super-resolution fluorescence microscopy is currently revolutionizing cell biology research. Its capacity to break the resolution limit of around 300 nm ...

De Novo Generation of Somatic Stem Cells by YAP/TAZ

De Novo Generation of Somatic Stem Cells by YAP/TAZ

从头用狂吠/狂暴法生成体细胞干细胞

Here we present protocols to isolate primary differentiated cells and turn them into stem/progenitor cells (SCs) of the same lineage by transient ...

IR-TEx: An Open Source Data Integration Tool for Big Data Transcriptomics Designed for the Malaria Vector Anopheles gambiae

IR-TEx: An Open Source Data Integration Tool for Big Data Transcriptomics Designed for the Malaria Vector Anopheles gambiae

IR-TEx：专为疟疾病媒阿诺菲斯甘巴病设计的大数据转录组学的开源数据集成工具

IR-TEx is an application written in Shiny (an R package) that allows exploration of the expression of (as well as assigning functions to) transcripts ...

Worm-align and Worm_CP, Two Open-Source Pipelines for Straightening and Quantification of Fluorescence Image Data Obtained from Caenorhabditis elegans

Worm-align and Worm_CP, Two Open-Source Pipelines for Straightening and Quantification of Fluorescence Image Data Obtained from Caenorhabditis elegans

蠕虫对齐和Worm_CP，两个开源管道，用于从卡诺哈布迪蒂斯精英获得的荧光图像数据的直化 和定量

An issue often encountered when acquiring image data from fixed or anesthetized C. elegans is that worms cross and cluster with their neighbors. This ...

Assessment of de novo Protein Synthesis Rates in Caenorhabditis elegans

Assessment of de novo Protein Synthesis Rates in Caenorhabditis elegans

卡诺哈布迪蒂斯 伊利根斯新蛋白合成率评估

Maintaining a healthy proteome is essential for cell and organismal homeostasis. Perturbation of the balance between protein translational control and ...

从头 使用核糖体分析数据识别主动翻译的开放阅读框

从头使用核糖体分析数据识别主动翻译的开放阅读框