This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What is a transcriptome?
Transcriptomics is the study of the expression of genes (transcription) or the study of the transcriptome. A transcriptome is the sum total of all the RNA and their quantity in a cell or a population of cells . There are two main technologies used to study transcriptomes, micro-arrays and RNA sequencing. RNA-seq is recently developed high-throughput method of quantifying and mapping transcriptomes and has many benefits over the older micro-array technology .
What is RNA sequencing?
RNA sequencing (RNA-seq) is based around recently developed deep-sequencing technologies (e.g. Illumina, SOLiD, 454). The general method is to convert a population of RNA to more stable cDNA fragments that have adapters at one or both ends . Then either with or with amplification these fragments are sequenced to obtain short reads (30 - 500 bp). These read are then either aligned to a reference genome or assembled de novo to produce a genome-wide transcription map . This map consist of information on the transcriptional structure and level of each gene in the genome.
How is this applicable to my project?
Knowing a single cell's or a tissue's transcriptome on its own is not particularly informative to how a process works. However, comparing the transcriptomes of two different cell types or between a wild type and mutant can be critical in understanding the inner workings of a particular process. In particular, I am interested in comparing the transcriptomes of wild type mice to GALT knock-out mutants when fed a galactose free diet. This will help identify genes that are differentially regulated when GALT is knocked out. Using this information we may be able to identify novel interacting proteins or possible novel functions of GALT (new metabolic roles or regulation roles). Thus, understanding the broader role of GALT will help develop treatments which can greatly reduce the risk of galactosemia phenotypes.
1. Wang et al. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63