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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.
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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing.

Jiao Cao1, Zhong Zheng1, Di Sun1

  • 1Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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|January 16, 2024
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Summary
This summary is machine-generated.

Spatial RNA sequencing using Decoder-seq enhances mRNA detection sensitivity and resolution. This breakthrough technology maps gene expression in tissues, aiding in understanding complex biological systems and disease progression.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • High-resolution spatial transcriptomics often struggles with sensitive mRNA detection.
  • Existing methods face limitations in balancing resolution and sensitivity for comprehensive gene expression analysis.

Purpose of the Study:

  • To introduce Decoder-seq, a novel dendrimeric DNA coordinate barcoding method for spatial RNA sequencing.
  • To achieve both high sensitivity and high resolution in mRNA detection for advanced spatial transcriptomics.

Main Methods:

  • Development of Decoder-seq combining dendrimeric nanosubstrates with microfluidic coordinate barcoding.
  • Achieving high DNA density on spatial arrays, approximately ten times higher than previous methods.
  • Application of Decoder-seq to mouse olfactory bulbs, hippocampus, and human renal cell carcinomas.

Main Results:

  • Decoder-seq significantly improved the detection of lowly expressed olfactory receptor genes in mouse olfactory bulbs.
  • Discovery of a unique layer enrichment pattern for two olfactory receptor genes.
  • Construction of a spatial single-cell atlas of the mouse hippocampus, revealing dendrite-enriched mRNAs.
  • Dissection of the heterogeneous tumor microenvironment in human renal cell carcinomas.
  • Identification of spatial gradient-expressed genes related to epithelial-mesenchymal transition for prognosis prediction.

Conclusions:

  • Decoder-seq offers a powerful tool for sensitive and high-resolution spatial transcriptomics.
  • The technology enables detailed analysis of gene expression in complex tissues and disease contexts.
  • Decoder-seq has the potential to advance our understanding of neurobiology and cancer biology.