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

Expression Data


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 Reflect

Explain 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



UAG - Stop and Reflect

Develop a hypothesis about shoot development using expression data. Respond in your journal




UAG - Stop and Reflect

What does it mean to assemble the transcriptome? Record how and why sequence data is assembled. Respond in your journal


UAG - Stop and Reflect

Why might you need the files with the assembly data if you have the Blast Chamaecrista site available to you? Respond in your journal