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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. 
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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 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.
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RNA Structure01:23

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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.
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Related Experiment Video

Updated: Feb 3, 2026

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis
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Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

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Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human

T L Masters1, C A Hilker2, P R Jeraldo3

  • 1Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.

Journal of Microbiological Methods
|October 18, 2018
PubMed
Summary

Metatranscriptomic studies offer insights into infectious diseases. Comparing RNA-Seq kits for clinical samples revealed the NuGEN Ovation SoLo kit is better for microbial RNA, while Illumina TruSeq excels for host RNA.

Keywords:
Gene expressionPeriprosthetic joint infectionRNA sequencingcDNA library preparation

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RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
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Area of Science:

  • Microbiology and Genomics
  • Infectious Disease Diagnostics
  • Metatranscriptomics

Background:

  • Metatranscriptomic studies analyze gene expression in microbial communities and hosts.
  • These studies are promising for infectious disease diagnostics but face challenges with low RNA yield and quality in clinical specimens.
  • Low microbial RNA quantity is a significant hurdle for accurate pathogen detection and characterization.

Purpose of the Study:

  • To compare the performance of two commercial stranded cDNA library preparation kits for metatranscriptomic analysis.
  • To evaluate their suitability for analyzing RNA from clinical samples, specifically synovial and sonicate fluids from a periprosthetic joint infection.
  • To determine which kit provides more effective transcriptomic data for microbial pathogens versus host RNA.

Main Methods:

  • RNA extraction from synovial and sonicate fluids of a patient with periprosthetic joint infection.
  • Comparison of two commercially available stranded RNA sequencing library preparation kits: NuGEN Ovation SoLo RNA-Seq System and Illumina TruSeq Stranded Total RNA.
  • Analysis of the resulting transcriptomic data to assess yield and quality for both microbial and human RNA.

Main Results:

  • The NuGEN Ovation SoLo RNA-Seq System yielded more useful transcriptomic data for the infecting bacterium.
  • The Illumina TruSeq Stranded Total RNA kit provided more useful human transcriptomic data.
  • Both kits demonstrated differential performance in capturing microbial versus host RNA signals.

Conclusions:

  • Kit selection is critical for optimizing metatranscriptomic analysis in clinical settings with limited RNA.
  • The NuGEN Ovation SoLo kit is advantageous for studies focusing on microbial pathogens in infection diagnostics.
  • The Illumina TruSeq Stranded Total RNA kit is more suitable for host-focused transcriptomic analysis in similar clinical scenarios.