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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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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
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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress.

Michael Hagemann-Jensen1, Christoph Ziegenhain1, Rickard Sandberg2

  • 1Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

Nature Biotechnology
|May 31, 2022
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Summary
This summary is machine-generated.

Smart-seq3xpress enhances single-cell RNA sequencing by reducing costs and increasing throughput. This method provides full-transcript coverage, revealing crucial isoform variations in cell types.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Current single-cell RNA sequencing (scRNA-seq) methods often compromise full-transcript coverage and sensitivity for high cellular throughput.
  • There is a need for scRNA-seq techniques that balance throughput with comprehensive gene expression analysis.

Purpose of the Study:

  • To introduce Smart-seq3xpress, a miniaturized and streamlined version of the Smart-seq3 protocol.
  • To improve cellular throughput and reduce reagent consumption in full-transcript single-cell RNA sequencing.
  • To enable the detailed characterization of cell types and isoform variations.

Main Methods:

  • Miniaturization and streamlining of the Smart-seq3 protocol to create Smart-seq3xpress.
  • Application of Smart-seq3xpress to analyze peripheral blood mononuclear cells.
  • Comparison of Smart-seq3xpress with droplet-based single-cell RNA sequencing methods.

Main Results:

  • Smart-seq3xpress significantly reduced reagent use and increased cellular throughput.
  • Analysis of peripheral blood mononuclear cells generated a granular cell atlas, identifying common and rare cell types.
  • Full-transcript coverage by Smart-seq3xpress revealed cell-type-associated isoform variations, unlike RNA-end sequencing methods.

Conclusions:

  • Smart-seq3xpress offers a powerful approach for high-throughput, full-transcript single-cell RNA sequencing.
  • The method enhances the ability to discover and characterize cell types and their unique isoform expression patterns.
  • Smart-seq3xpress provides deeper biological insights compared to existing droplet-based scRNA-seq techniques.