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相关概念视频

RNA-seq03:21

RNA-seq

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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...
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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相关实验视频

Updated: Jan 14, 2026

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
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一个转录可塑性意识的框架用于RNA-seq差异表达分析.

Cheng Bei1, Xiaoman Wang2, Mingyu Gan3

  • 1Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, 138 Yixueyuan Rd, Xuhui District, Shanghai 200032, China.

Briefings in bioinformatics
|October 20, 2025
PubMed
概括

转录性可塑性 (TP) 偏差基因表达分析. 一个新的TP意识框架调整折叠变化,改善差异表达 (DE) 结果并揭示细菌中的新生物学见解.

关键词:
在RNA-seqqq.细菌 细菌 细菌是一种细菌.不同的表达分析分析差异表达分析.这种细菌名为mycobacterium.转录性可塑性 转录性可塑性

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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相关实验视频

Last Updated: Jan 14, 2026

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科学领域:

  • 微生物学 微生物学
  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.

背景情况:

  • 转录基因数据的差异表达 (DE) 分析评估了全基因组基因响应.
  • 转录可塑性 (TP),基因表达与环境变化的变化,尚未被探索其对DE分析的影响.

研究的目的:

  • 调查TP对DE分析的影响.
  • 引入一个TP意识的框架,以提高DE结果的解释.

主要方法:

  • 相关基因表达折叠变化与TP跨越238个实验在Mycobacterium结核病 (Mtb) 和大肠杆菌 (E. coli).
  • 应用局部估计的散射图平滑到TP来调整基因表达折叠变化.
  • 进行调整的DE分析以确定响应途径.

主要成果:

  • 在DE分析中确定了固有的偏差,有利于高TP基因和忽视低TP基因.
  • 调整后的DE分析揭示了具有更高统计学意义和丰富度的新响应途径,特别是对于低TP基因.
  • 具体发现包括mtb对贝达基林 (胆固醇降解) 的反应,linezolid (乙酸代谢抑制) 和巨菌感染 (脂肪酸代谢上调,辅因子生物合成下调).

结论:

  • TP-aware框架通过纠正固有的转录变异性来使DE分析正常化.
  • 这种调整策略适用于各种细菌物种,并且与各种RNA-seq量化方法兼容.
  • 这种方法可以更好地发现生物相关的基因表达变化,特别是那些涉及低转录可塑性基因的基因.