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RNA-seq

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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Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.

Heesun Shin¹, Martin Hirst, Matthew N Bainbridge

¹Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada. heesuns@sfu.ca

|July 10, 2008

Summary

High-throughput sequencing of Caenorhabditis elegans revealed novel transcripts and splice variants in its first larval stage. This advanced method provides a comprehensive transcriptome profile, offering insights into developmental complexity.

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Published on: April 8, 2017

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Combined Nucleotide and Protein Extractions in Caenorhabditis elegans

Combined Nucleotide and Protein Extractions in Caenorhabditis elegans

Published on: March 17, 2019

Area of Science:

Developmental Biology
Genomics
Molecular Biology

Background:

Transcriptome profiling of Caenorhabditis elegans (C. elegans) at the first larval stage using high-throughput pyrosequencing.
Generation of extensive expressed sequence tag (EST) data for discovery of novel transcripts and splice variants specific to early development.
Demonstration of next-generation sequencing (NGS) as an efficient methodology for transcriptome analysis.

Purpose of the Study:

To comprehensively profile the transcriptome of C. elegans during its first larval stage.
To identify novel transcripts, alternative splice variants, and non-coding RNAs potentially specific to this developmental stage.
To showcase the utility of high-throughput sequencing for genome-wide transcript verification.

Main Methods:

Application of high-throughput pyrosequencing to generate over 30 million bases of ESTs from C. elegans first larval stage.
Bioinformatic analysis of ESTs to identify novel genetic structures, alternative splicing events, and transcript extensions.
Integration of serial analysis of gene expression (SAGE) data to predict stage-specific novel transcripts.

Main Results:

Approximately 14% of novel ESTs map to unannotated genomic regions, suggesting novel genetic structures.
Identification of numerous ESTs in intergenic and intronic regions, potentially representing novel small genes or splice variants.
Discovery of conserved intergenic and intronic ESTs, likely indicating non-coding RNAs, and ESTs suggesting alternative splicing and transcript extensions.

Conclusions:

High-throughput sequencing efficiently captures transcriptional activities in the C. elegans first larval stage.
This methodology enables high-throughput, genome-wide verification of both known and novel transcripts.
The study enhances the C. elegans transcriptome profile, providing insights into evolutionary and biological complexity.