Illumina/Solexa whole transcriptome sequencing provides information about gene expression, as well as nucleotide sequence. The more copies of a specific transcript in an RNA isolation, the more times that transcript will be sequenced. Transcript abundance correlates directly with gene expression levels.
Tissues used in expression analysis
Transcriptome libraries from shoots, roots, and nodules of Chamaecrista fasciculata plants at different stages of development were used for Illumina/Solexa sequencing. Before sequencing, mRNA was purified from the total RNA. You can get more information about the stages by downloading the linked PowerPoint slides.
Shoot, root, and nodule libraries (PowerPoint 2007 (.pptx) 14MB Jan19 09)
JMP Genomics exercise to get you thinking about gene expression
JMP Genomics is a statistical software package that lets you look for gene expression patterns. The two links that follow provide the directions and data needed to visualize patterns in gene expression among the different Chamaecrista tissue types. Work through this exercise before you go on to plan your own strategy for working with the expression data. The software is available for all faculty and students in the Biology Department. It is currently on the machines in CMC 109 and the Biology Computer Lab. As a student in the class, you can download your own copy from the COLLAB server folder (Departments/Biology) onto a Windows machine.
JMP Genomics Gene Expression Exercise (Microsoft Word 2007 (.docx) 38kB Feb7 11)
Data File for JMP Genomics Gene Expression Exercise (Text File 5.5MB Jan9 11)
Paper on Analyzing Gene Expression (Acrobat (PDF) 4.7MB Jan11 10) the figures may be helpful as you reflect on the results of your JMP analysis.
Enter your conclusions from your JMP Genomic gene expression analysis in your electronic notebook.
Puzzled?Not sure what all the columns are in the expression table? Click here for help
The expression data is available in a number of formats. Reads per million calibrates the data across samples.
Expression Data - Unique reads per million (Text File 5.5MB Jan11 10) - Only the latest version of Excel will show you all the data.
Expression Data - Total unique reads (Text File 1.2MB Jan11 10) - Only the latest version of Excel will show you all the data.
Expression Data - Reads per million (Text File 5.5MB Jan11 10) - Only the latest version of Excel will show you all the data.
Expression Data - Reads (Text File 1.2MB Jan11 10) - Only the latest version of Excel will show you all the data.
UAG - Stop and ReflectExplain how the number of reads of a given sequence provides you with useable information about gene expression. Describe two other ways you could determine the level of expression of specific genes. Respond in your journal
Asking questions with expression data
- What is the overall pattern of gene expression for the shoot transcriptome?
- Using the youngest shoot library, can you rank the genes based on expression and plot your results?
- What happens if you then plot the data for the other shoot libraries? How do they compare to each other?
- Can you compare expression patterns in roots, shoots, and nodules? How might you organize and present the data?
- If you worked on candidate genes, can you use that information to look at expression patterns of specific genes as a function of tissue type and developmental stage?