To submit a microarray hybridization request to HCI's Microarray and Genomic Analysis Core Facility:

1. Start the GNomEx microarray request submission wizard by clicking on either the Submit Experiment Request button in the Experiments section of the home page of the application environment or the smaller button with the same label along the top row of the application.

The New Experiment Request module will open with the Experiment setup tab selected.

2. Select the appropriate lab group, your name and the appropriate account number in the three drop-down fields at the top of the Experiment setup tab.

3. Select the applicable service from among the (4) Select a service radio buttons. A short summary of the applications possible with each service is displayed next to that service in the Application Options column.

4. Do one of the following as appropriate:

• If your experiment is part of an existing project, select that project in the drop-down field at the bottom of this tab.

• If your experiment is part of a new project (or in other words there are no other experiments in the system assigned to this project), select the New project radio button. The New Project window will appear. Enter the appropriate project information on the window and click the Save button. (See Adding a New Project While You Are Entering a Microarray Hybridization Request for more information.) The New Project window will close and this new project will automatically be selected in the project drop-down field.

The experiment information and data for services for the same project will be stored together in the experiment repository, so this allows you to organize your experiments appropriately.

You may also edit an existing project at this point as well — see Editing an Existing Project While Entering a Microarray Hybridization Request.

5. Click on the Sample Setup tab or click on the Next button at the bottom left side of the window.

The Sample Setup tab will be selected.

6. Enter the number of samples you are submitting and select the category, source organism and nucleic acid extraction method that apply to request in the fields on the Sample setup tab.

A default value will be selected for the nucleic extraction method based on the category selected, but you can still select a different method if appropriate. The options available in that field will depend on the category selected.

7. Click on the Annotations tab or click on the Next button at the bottom left side of the window.

The Annotations tab will be selected.

8. Adding annotations is optional. If you would like to add annotations about certain characteristics of the samples being submitted, check the square next to each applicable characteristic in the list on the left hand side of the tab.

9. (Also optional) Add a description of how the samples differ from each other in the large text field on the right side of the tab.

10. Click on the Sample View tab or click on the Next button at the bottom left side of the window.

The Sample View tab will be selected.

11. Enter/edit the appropriate data about each of the samples you will be submitting in the grid on the Sample View tab. See The Sample View Tab (New Experiment Request Module) for a description of the grid and its associated buttons and columns. Also see Working With the List of Samples You Will Be Submitting for Microarray Hybridization for specific instructions to tasks related to this list of samples.

There will already be some samples appearing in the grid on the Sample View tab. The information entered in these samples (including the number of samples appearing in the grid) is based on the data entered previously in the process. However, you can still make changes to this list as required, including adding and removing samples to/from the list. In most cases, you will simply need to provide the missing required information about each of the samples to the rows already appearing in the grid — see Editing a Sample from the List of Samples You Will Be Submitting for Microarray Hybridization.

Additional columns will appear in the Samples grid based on the settings selected on the Annotations tab. This is where you can provide the specific annotations about each of the samples in the areas you indicated on that tab.

Required fields that do not have any data entered in them yet will appear with a yellow background until data is entered. These required fields include the Sample Name, Label (if applicable to the type of microarray hybridization you are requesting), Concentration and any sample characteristics you indicated you wanted to include annotations about the samples on. You will not be able to move on to the next step in the request process until there are no more fields with a yellow background in the grid.

If you have multiple samples to enter and the information about these samples is already recorded in a spreadsheet, you may upload that spreadsheet to have the values entered automatically instead of having to enter them manually — see Uploading a Sample Sheet.

12. Click on the Hyb setup tab or click on the Next button at the bottom left side of the window.

The Hyb setup tab will be selected.

13. Select the appropriate general settings for the hybridizations you are requesting in the dropdown fields and radio buttons on the Hyb setup tab. See The Hyb Setup Tab (New Experiment Request module) for a description of the fields on this tab.

14. Click on the Hyb View tab or click on the Next button at the bottom left side of the window.

The Hyb View tab will be selected.

15. Assign each of the samples to a specific slide and coordinate within that slide for hybridization by dragging the appropriate sample from one of the two lists on the left side of the window to the appropriate location in the hybridization list on the right. Each hybridization will require a Cy3 sample. Depending on your request, you may or may not need to also indicate a Cy5 Sample for each. For some requests, you may also need to select the slide to be used for each hybridization. If all of the default settings are correct, simply click on the grid to activate the Next button.

Just as with the samples on the Sample View tab, there will already be some hybridizations appearing in the grid on the Hybridizations tab. The information entered in these hybridizations (including the number of hybridizations appearing in the grid) is based on the data entered on the Hyb setup tab. The samples may also already be assigned to default locations on the slides. As before, you can still make changes to this list as required, including adding and removing hybridizations to/from the list or moving a sample from one location to another — see Working With the List of Hybridizations You Will Be Requesting for specific instructions to tasks related to this list of hybridizations. However, in most cases, you will simply need to assign the appropriate samples to each slide and coordinate as directed above.

As with the samples grid, required fields that do not have any data entered in them yet will appear with a colored background (green or red) until data is entered (meaning that every hybridization should have a Cy3 sample and a Cy5 sample assigned to it. You will not be able to move on to the next step in the request process until all of these fields are filled in. Each sample in Cy3 and Cy5 lists on the left that has already been placed in the Hybridizations grid will have a checkmark appear next to it in the list.

16. Click on the Visibility tab or click on the Next button at the bottom left side of the window.

The Visibility tab will be selected.

17. (Optional) Change the level of the visibility of the experiment by selecting the appropriate radio button (indicating whether the experiment should only be visible to the submitter and lab PI, to all the members of the lab group, any lab group at a specified institution, or anyone at all) and/or adding specific collaborators to the list at the bottom of the window by selecting their name in the dropdown field and clicking on the plus button next to that field.

This tab controls who will be able to see the experiment results and analysis in GNomEx. These settings can be changed later in the Experiments module.

18. Click on the Confirm tab or click on the Next button at the bottom left side of the window.

The Confirm tab will be selected.

19. Review the request summary information as displayed on the window to make certain it is correct. If changes are needed, correct them by returning to the applicable tab.

20. Once you are satisfied that your request is entered correctly, click on the Submit button on the bottom left side of the window. The request will be submitted to the HCI Microarray and Genomic Analysis Core Facility and a confirmation that the submission has occurred will appear on the window. You will also receive an email confirming the receipt of your submission.

21. Click OK to clear the request confirmation dialog. The experiment summary for this request in the Experiments module will appear. This is where you will be able to print the request.

22. Click on the Printable form hyperlink to generate a printable copy of the request.

A separate browser window will open (outside the application desktop environment) with a summary of the request you just submitted.

23. Print a copy of the request using the browser's print function and bring the printed copy of that request together with your samples to the HCI Microarray and Genomic Analysis Core Facility.

The Next or Continue button at the bottom of one of the tabs is grayed out and doesn't do anything when I click on it — This button will only become available for use after you have entered all of the required information on that tab. In order to activate it, first be certain you have entered all of the required information on the current tab. To assist you in discovering required information that has been missed, when a required value in a grid has been left blank, that field will be displayed in pink. This will not happen with required fields that do not appear as columns in a grid, however. The button may also be inactive if you have skipped forward in the wizard and left a required field on a previous tab blank. If you are certain you have entered all of the required information on the current tab, review the previous tabs in the wizard to make certain you have entered all of the required information on them as well.