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Related Concept Videos

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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Mesh Analysis with Current Sources01:10

Mesh Analysis with Current Sources

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Mesh analysis becomes simpler when analyzing circuits with current sources, whether independent or dependent. The presence of current sources reduces the number of equations required for analysis. Two cases illustrate this:
Current Source in One Mesh: The analysis process is straightforward when a current source is found in only one mesh within the circuit. Mesh currents are assigned as usual, with the mesh containing the current source excluded from the analysis. Kirchhoff's voltage law...
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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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Alternative RNA Splicing02:18

Alternative RNA Splicing

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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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Updated: Jan 23, 2026

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
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Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

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Current best practices in single-cell RNA-seq analysis: a tutorial.

Malte D Luecken1, Fabian J Theis2,3

  • 1Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.

Molecular Systems Biology
|June 21, 2019
PubMed
Summary
This summary is machine-generated.

This study provides a best-practice workflow for single-cell RNA sequencing (scRNA-seq) analysis. It guides users through pre-processing and downstream analysis steps, integrating current recommendations for accurate gene expression studies.

Keywords:
analysis pipeline developmentcomputational biologydata analysis tutorialsingle‐cell RNA‐seq

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Single-cell RNA sequencing (scRNA-seq) offers high-resolution gene expression analysis.
  • A growing user base requires efficient and up-to-date analysis workflows.
  • The increasing number of analysis tools complicates workflow selection.

Purpose of the Study:

  • To detail a typical scRNA-seq analysis workflow.
  • To provide best-practice recommendations based on comparative studies.
  • To serve as a tutorial for new and established researchers.

Main Methods:

  • Quality control, normalization, data correction, feature selection, and dimensionality reduction.
  • Cell- and gene-level downstream analysis.
  • Integration of best-practice recommendations into a unified workflow.
  • Application of the workflow to a public dataset for practical illustration.

Main Results:

  • A comprehensive workflow for scRNA-seq data analysis is presented.
  • Best-practice recommendations are formulated and integrated.
  • A documented case study demonstrates the workflow's application.

Conclusions:

  • The developed workflow assists researchers in navigating scRNA-seq analysis.
  • It serves as a valuable resource for updating existing analysis pipelines.
  • Facilitates reproducible and accurate gene expression studies.