Chapter title |
Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species.
|
---|---|
Chapter number | 1 |
Book title |
Yeast Functional Genomics
|
Published in |
Methods in molecular biology, January 2016
|
DOI | 10.1007/978-1-4939-3079-1_1 |
Pubmed ID | |
Book ISBNs |
978-1-4939-3078-4, 978-1-4939-3079-1
|
Authors |
Wang, Can, Schröder, Markus S, Hammel, Stephen, Butler, Geraldine, Schröder, Markus S., Can Wang, Markus S. Schröder, Stephen Hammel, Geraldine Butler |
Abstract |
The ability to extract, identify and annotate large amounts of biological data is a key feature of the "omics" era, and has led to an explosion in the amount of data available. One pivotal advance is the use of Next-Generation Sequencing (NGS) techniques such as RNA-sequencing (RNA-seq). RNA-seq uses data from millions of small mRNA transcripts or "reads" which are aligned to a reference genome. Comparative transcriptomics analyses using RNA-seq can provide the researcher with a comprehensive view of the cells' response to a given environment or stimulus.Here, we describe the NGS techniques (based on Illumina technology) that are routinely used for comparative transcriptome analysis of fungal species. We describe the entire process from isolation of RNA to computational identification of differentially expressed genes. We provide instructions to allow the beginner to implement packages in R such as Bioconductor. The methods described are not limited to yeast, and can also be applied to other eukaryotic organisms. |
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Student > Doctoral Student | 1 | 3% |
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Immunology and Microbiology | 1 | 3% |
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