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Related Concept Videos

RNA-seq03:21

RNA-seq

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 microarray-based...

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Related Experiment Video

Updated: May 28, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
10:22

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

Protocol for simultaneous profiling of transcription start sites and full-length transcripts from low-input samples

Diego Rodriguez-Terrones1, Marlies E Oomen1, Maria-Elena Torres-Padilla2

  • 1Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany.

STAR Protocols
|May 26, 2026
PubMed
Summary

Smart-seq+5' is a new low-input protocol for full-length transcript profiling and precise transcription start site (TSS) identification. This method enhances sensitivity for both polyadenylated and non-polyadenylated transcripts.

Keywords:
Gene ExpressionGenomicsMolecular BiologyRNAseq

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Last Updated: May 28, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

  • Molecular Biology
  • Genomics
  • Transcriptomics

Background:

  • Cap analysis of gene expression (CAGE) identifies transcription start sites (TSS) and promoter activity.
  • Existing methods like CAGE require substantial RNA input and cannot profile entire transcript bodies.
  • There is a need for low-input methods capable of simultaneous full-length transcript and TSS profiling.

Purpose of the Study:

  • To present Smart-seq+5', a novel low-input protocol for characterizing full-length transcripts.
  • To enable simultaneous identification of precise transcription start site (TSS) locations.
  • To improve upon existing transcriptomic techniques by increasing sensitivity and accommodating diverse RNA types.

Main Methods:

  • RNA extraction with optional in vitro polyadenylation.
  • Reverse transcription and 5' capture.
  • Tn5 tagmentation for comprehensive transcript coverage.
  • Computational analysis for data interpretation.

Main Results:

  • Smart-seq+5' successfully characterizes full-length transcripts.
  • Precise TSS locations are identified concurrently with transcript profiling.
  • The protocol demonstrates improved sensitivity compared to standard methods.
  • Applicable to both polyadenylated and non-polyadenylated RNA samples.

Conclusions:

  • Smart-seq+5' is an effective low-input method for comprehensive transcriptomic analysis.
  • This protocol advances the ability to study gene expression regulation at the TSS and transcript body level.
  • Smart-seq+5' offers enhanced sensitivity and versatility for various RNA samples.