Microarray quick start tutorial

SNP MICROARRAYEXPRESSION MICROARRAY
Contributed by Karen Klyczek, University of Wisconsin-River Falls

Text below is a general summary of procedures for running SNP and expression microarrays, designed to get you up and running quickly. Video tutorials linked below provide considerably more detail on the generation and interpretation of microarray results, including instructions on how to construct microarray data files for Case It v7.0.4.

SNP MICROARRAYS

Video tutorial on SNP microarrays

General procedure for running SNP microarrays:

1. Use the Chip button on the button bar to open a SNP chip file.  Browse the Case It v704 folder, Cases > Microarray cases > SNP microarrays and select the file for a particular case.   This will open the DNA chip window. Click the Load button to load the probes and DNA samples.

[Note: The file SNP tutorial.csv is now inside a separate folder, located inside the SNP microarray folder. This file is used if you want to follow along with the tutorial video.]

2. On the silver button bar, click Chip > Run chip to run the microarray.  The probes are organized as SNP pairs.  The fluorescence intensity value for each probe is shown in the labels to the right of the window, and based on the relative fluorescence of the two paired probes, a genotype for that SNP is called.

3. To view the results for each sample, click on the sample names in the O&P window, or use the chip navigation window to select each sample.

4. To compare two samples and identify SNP differences, click on the two samples you want to compare in the O&P window.   The last two samples clicked will be compared.  Note that “This chip” (currently selected sample) and “Last chip” (previously selected sample) are indicated below the labels.  Click the Chip button and select “SNP chip > Compare last two SNP chips selected.” Cells corresponding to genotype differences between the two samples will be highlighted in yellow.

5. To find out where in the human genome a particular SNP is located, click on the label or the spot to highlight the spot, and then right click on the spot.  From the menu that appears, select either:- Send the probe sequence for BLAST analysis, to compare it with known sequences in the NCBI database.  Do the BLAST results help you identify the nature of the SNP site?  There are two options for doing this:

  • Copy the probe sequence to the clipboard and open the NCBI BLAST web site.  Click in the sequence box and paste, and the probe sequence should appear.  Click the BLAST button at the bottom of the page and the results will appear in a new window.
  • Send the probe sequence to the BLAST server and return an abbreviated BLAST result containing just the first 15 matches.  This result should open automatically in your default browser.

Copy the probe ID name and open the dbSNP database site to search the SNP ID. Click in the search box and paste the ID from the clipboard.   Click Go to search for that SNP. If you get a search result, click on the name to go to the full SNP page.  Does the information on that page help you identify the nature of the SNP?  Some of the standard information includes:  chromosome location, allele statistics, gene association, clinical relevance.

[Note: The format of this page has changed considerably since the video was produced, so the information in from 14:20 to 20:38 is obsolete, in terms of how you can find that particular information.]

EXPRESSION MICROARRAYS

Video tutorial for expression microarrays

General procedure for running expression microarrays:

1. Use the Chip button on the button bar to open a SNP chip file.  Browse the Case It v704 folder, Cases > Microarray cases > Expression microarrays and select the file for a particular case.   This will automatically open the DNA chip window and load the probes and DNA samples. There is one green-labeled DNA sample (control) and one red-labeled sample (experimental)

2. On the silver button bar, click Chip > Run chip to run the microarray . 

3. To view the results for each sample, click on the sample names in the O&P window, or use the chip navigation window to select each sample.

4. To combine the red and green results, click on the Chip button > Compare > Combine red and green data. This will yield a spectrum of red, green, and yellow spots. Red indicates increased expression of that gene in the experimental sample, while green indicates decreased expression in the experimental sample. Yellow indicates equal expression in both samples.

5. The probe spots can be rearrange to group similar colors together, making it easier to examine groups of genes with similar behavior. Click on the Chip button > Compare > group results according to color.

6. To learn more about the gene associated with a particular spot, click on the spot or corresponding cell, and right click on the spot to open the menu. The options are:

  • Send the probe sequence for BLAST analysis, to compare it with known sequences in the NCBI database.  Do the BLAST results help you identify the nature of the SNP site?  There are two options for doing this:
  • Copy the gene name and open the NCBI OMIM database site to search for information about that gene. Click in the search box and paste the gene name from the clipboard. Click Go to search for that gene. Click on any of the search results to go to the information page for that gene.