Difference between revisions of "20.109(S20):Examine qPCR results and complete data analysis (Day8)"
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In this figure, the DLD-1 (left column) and A549 (right column) datasets were compared and the top 100 GO terms that contained significantly enriched terms were identified. This is different from the figures you generated in the previous exercises as these data are not specific to up or down-regulated genes, rather the overall change across the genes within the GO term was considered. Now that we understand the scope of the data, let's look closer at the specific information provided in the figure. | In this figure, the DLD-1 (left column) and A549 (right column) datasets were compared and the top 100 GO terms that contained significantly enriched terms were identified. This is different from the figures you generated in the previous exercises as these data are not specific to up or down-regulated genes, rather the overall change across the genes within the GO term was considered. Now that we understand the scope of the data, let's look closer at the specific information provided in the figure. | ||
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| + | First the results shown in blue and red represent significance according to the p-value (blue to red scalebar to the right of the figure). In this representation the data are shown as either not significant (blue = 0 on scalebar) or significant (red = 1 on scalebar). Given that the bars in the top row are red for both DLD-1 and A549, the interpretation concerning the data for this GO term (GO term labels are included to the immediate right of the image, black illegible text) is that there are significant changes in expression for the genes within this GO term in both DLD-1 and A549. As a reminder, this does not denote up or down, just that gene expression is different compared to the no etoposide treatment. | ||
==Protocols== | ==Protocols== | ||
Revision as of 14:49, 26 March 2020
Introduction
Throughout Module 2 you have used two datasets to study the effect of etoposide treatment on cancer cell lines (DLD-1 and A549). In the previous exercises you examined gene expression in each cell line. Today you will use the skills learned to compare gene expression across DLD-1 and A549.
As an introduction to how you will discuss and interpret the data in your Research article, let's work though the below figure:
In this figure, the DLD-1 (left column) and A549 (right column) datasets were compared and the top 100 GO terms that contained significantly enriched terms were identified. This is different from the figures you generated in the previous exercises as these data are not specific to up or down-regulated genes, rather the overall change across the genes within the GO term was considered. Now that we understand the scope of the data, let's look closer at the specific information provided in the figure.
First the results shown in blue and red represent significance according to the p-value (blue to red scalebar to the right of the figure). In this representation the data are shown as either not significant (blue = 0 on scalebar) or significant (red = 1 on scalebar). Given that the bars in the top row are red for both DLD-1 and A549, the interpretation concerning the data for this GO term (GO term labels are included to the immediate right of the image, black illegible text) is that there are significant changes in expression for the genes within this GO term in both DLD-1 and A549. As a reminder, this does not denote up or down, just that gene expression is different compared to the no etoposide treatment.
Protocols
Part 1: Analyze RNA-seq data
Today you will complete your analysis of the RNA-seq data sets!
Complete Exercise #4 developed by Amanda Kedaigle, Anne Shen & Prof. Ernest Fraenkel. In this exercise, compare the RNA-seq results for DLD-1 and A549 to identify similarities and / or differences in gene expression that exist when cells are treated with etoposide.
Next day: Enrich candidate clones using fluorescence-activated cell sorter (FACS)
