相关实验视频

Updated: Jun 23, 2025

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

从新兴模型生物体的短读数据使用的转录组和差异性基因表达分析的新组装 - 一个简短的指南

Daniel J Jackson¹, Nicolas Cerveau², Nico Posnien³

¹University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany. djackso@gwdg.de.

Frontiers in zoology

|June 20, 2024

概括

建立一个 de novo 的参考转录组对于新兴的模型系统至关重要. 这本指南简化了这一过程,为研究人员提供建议和工具,为转录组组装和差异基因表达分析提供新的建议和工具.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
分子生物学分子生物学

背景情况:

高通量测序通过在各种模型系统中实现基因组和转录组分析,使生物研究民主化.
分析大型测序数据集存在挑战,特别是对于缺乏既定基因组参考的新兴模型系统.
在新的模型生物体中进行基因和分子研究的重要第一步是De novo转录组组装.

研究的目的:

为研究人员提供关于新兴模型系统的de novo转录组组件的指南.
概述实验和生物信息学的挑战,并为组装转录组提供解决方案.
推分析原始测序数据和识别差异表达基因的工具.

主要方法:

从原始的短读测序数据中 De novo 转录组组.
生物信息管道开发和优化转录基因组组装.
使用组装的转录组引用进行差异基因表达分析.

主要成果:

识别de novo转录组组装中的关键挑战.
对装配工艺的实证优化的建议.
一个精心挑选的生物信息学工具,用于转录组组装和基因表达分析.

结论:

对于推进新兴模型系统的研究来说,de novo转录组组装是必不可少的.
这本指南为研究人员提供了导航转录组组装和基因表达分析的知识.
可访问的工具和方法使研究人员能够建立关键的基因组资源.

关键词:

标注注释标注注释在新的组装 De novo.不同基因表达的差异性新兴模型系统新兴模型系统基因组基因组基因组基因组基因组在RNA-seqqq.简短的阅读简短的阅读转录组组件组合

更多相关视频

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

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

Published on: November 1, 2014

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

相关概念视频

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...