What is a transcriptome?
A transcriptome is the RNA expressed in a cell, tissue or organ. Which genes are being transcribed depend on the environmental conditions and the stage of development of the organism. Chamaecrista
has one genome, but many transcriptomes. We isolated total RNA, but then selected for mRNA before sequencing our Chamaecrista
What types of RNA would you find in total RNA?
How might you separate mRNA from total RNA?
Which transcriptomes are you exploring?
You have access to whole transcriptome sequences from shoots, roots, and nodules of the Minnesota ecotype of Chamaecrista fasciulata
plants at different developmental stages. Because differences have been observed among Minnesota, Kansas, and Oklahoma ecotypes, you also have whole transcriptome sequences for shoots KS, and OK ecotypes. The Minnesota data alone can be used to analyze levels of gene expression. You can look for genetic variation among ecotypes by comparing the transcriptomes of MN, KS, and OK. Here's a summary of the sequencing results (PowerPoint 2007 (.pptx) 457kB Jan19 09)
. One of the first things you may notice is the vast amount of data available to you. The interface strategies are designed to reduce the how overwhelming data sets like this can seem when you are just getting started.
Pick a strategy and get started.