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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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DNA Agarose Gel Electrophoresis02:35

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Agarose gel electrophoresis is a laboratory technique commonly used to separate DNA fragments by size. However, it can also be used to isolate and purify DNA fragments using a gel extraction protocol.
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Bacterial RNA Polymerase00:43

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
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RNA Splicing01:32

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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 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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Eukaryotic RNA Polymerases00:58

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices
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Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices.

Gordon D Hoople1, Andrew Richards2, Yan Wu2

  • 1Department of Engineering, University of San Diego; ghoople@sandiego.edu.

Journal of Visualized Experiments : Jove
|April 10, 2018
PubMed
Summary
This summary is machine-generated.

Gel-seq enables simultaneous DNA and RNA library preparation from small cell samples. This novel hydrogel device allows researchers to perform both genomic and transcriptomic sequencing without splitting samples, reducing costs and complexity.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Transcriptomics

Background:

  • Recent advances allow DNA or RNA amplification and sequencing from small samples.
  • Standard protocols for genomic and transcriptomic library preparation are incompatible, forcing researchers to choose between DNA or RNA sequencing.
  • This limitation hinders comprehensive analysis of a single biological sample.

Purpose of the Study:

  • To introduce Gel-seq, a novel method for simultaneous DNA and RNA library preparation.
  • To provide a detailed protocol for fabricating the Gel-seq hydrogel device and generating paired DNA and RNA libraries.
  • To enable researchers to perform both genomic and transcriptomic sequencing on the same sample.

Main Methods:

  • Fabrication of a simple hydrogel device for sample processing.
  • A biological protocol utilizing commonly-used kits for whole-transcript amplification (WTA) and library preparation.
  • Simultaneous library preparation for both DNA and RNA from 100-1000 cells.

Main Results:

  • Gel-seq successfully generates paired DNA and RNA libraries from small cell inputs.
  • The method is designed for easy implementation in standard genetics laboratories.
  • The protocol uses widely available kits, familiar to researchers.

Conclusions:

  • Gel-seq overcomes the incompatibility of standard protocols, allowing simultaneous DNA and RNA sequencing.
  • This approach provides a cost-effective and efficient way to obtain comprehensive genomic and transcriptomic data from a single sample.
  • Gel-seq empowers researchers with the combined power of DNA and RNA sequencing without sample splitting.