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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...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

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 primer.
Since the...
Ribosome Profiling02:24

Ribosome Profiling

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
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Related Experiment Video

Updated: May 9, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and

Brian J Haas1, Alexie Papanicolaou2, Moran Yassour1,3

  • 1Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.

Nature Protocols
|July 13, 2013
PubMed
Summary
This summary is machine-generated.

This study presents the Trinity platform for de novo transcriptome assembly from RNA-seq data, enabling genome-independent analysis. It offers tools for transcript abundance, differential expression, and protein-coding gene identification in non-model organisms.

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Related Experiment Videos

Last Updated: May 9, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Area of Science:

  • Genomics
  • Bioinformatics
  • Transcriptomics

Background:

  • De novo transcriptome assembly from RNA-seq data allows gene expression studies without a reference genome.
  • This approach is crucial for non-model organisms, cancer research, and microbiome studies.

Purpose of the Study:

  • To describe the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms.
  • To present companion utilities for downstream transcriptomic analyses.

Main Methods:

  • Utilized the Trinity platform for de novo transcriptome assembly.
  • Employed RSEM for transcript abundance estimation.
  • Applied R/Bioconductor packages for differential gene expression analysis and protein-coding gene identification.

Main Results:

  • Provided a workflow for genome-independent transcriptome analysis using the Trinity platform.
  • Demonstrated the processing of an example dataset in under 5 hours.
  • Trinity software, documentation, and demonstrations are freely available online.

Conclusions:

  • The Trinity platform offers a comprehensive solution for de novo transcriptome assembly and downstream analysis.
  • This workflow facilitates transcriptomic research, particularly in organisms lacking a reference genome.