1 IMDS Tutorial Integrated Microarray Database System

2 IMDS User Interface Functions I. Logging in to the database. Logging in to the database. II. Entering a new experiment. Entering a new experiment. III. Searching for experiments. Searching for experiments. IV. Updating an experiment. Updating an experiment. V. Entering new sources. Entering new sources. VI. Entering new treatment categories. Entering new treatment categories. VII. Reviewing the file access log. Reviewing the file access log.

3 I. Logging in to the database Enter username and password and click on the Submit button. An introductory page will appear, with Welcome your name at the top.

4 I. Logon Screen:

5 I. Introductory Page:

6 II. Entering a New Experiment Click on the experiment list link on the sidebar menu. You will be taken to the experiment list page. Click on Create a New Experiment. You will be taken to the experiment creation page.

7 II. Experiment List Link:

8 II. Create a New Experiment:

9 II. Experiment Creation Page:

10 II. Entering a New Experiment Enter the information describing the experiment – section 1.section 1. Enter the information about the treatments used in the experiment – section 2.section 2. Enter the information about the samples used in the experiment – section 3.section 3. Enter the information about the arrays used in the experiment – section 4.section 4. Upload the files (raw data) for the experiment – section 5.section 5. Upload the files (analyzed data and general information) for the experiment – section 6.section 6.

11 II. Entering a New Experiment: Section 1 (Description) Enter the experiment name and a short abstract in the fields marked name and description. Enter the starting date for the experiment. For example, 03/31/03 or 03/31/2003. Select your research site and PI from the pull down menus. Select the type of experiment from the pull down menus. Select other if your experiment type is not listed. Click on the Submit button when you are finished. You will be taken back to the experiment list page.

12 II. Entering a New Experiment: Section 1 (Description)

13 II. Entering a New Treatment: Section 2 (Treatment List) From the experiment list page, click on the name of the experiment for which you want to enter a new treatment. From the description page for that experiment, click on the Treatment List link in the footer. You will be taken to the treatment creation page.

14 II. Entering a New Treatment: Section 2 (Treatment List)

15 II. Entering a New Treatment: Section 2 (Treatment List)

16 II. Entering a New Treatment: Section 2 (Treatment Creation Page)

17 II. Entering a New Treatment: Section 2 (Treatment Creation Page) Enter the treatment name and a short treatment description or treatment protocol in the fields marked Treatment Name and Treatment Description. Select your treatment category from the pull down menu. Click on the Submit button when you are finished. You will be taken back to the treatment list page.

18 II. Entering a New Treatment: Section 2 (Treatment Creation Page)

19 II. Entering a New Treatment: Section 2 (Treatment Creation Page)

20 II. Entering a New Treatment: Section 2 (Treatment List Page)

21 II. Entering a New Sample: Section 3 (Sample List) From the treatment list page (or from the description page for your experiment), click on the Sample List link in the footer. You will be taken to the sample list page. Click on Create a New Sample. You will be taken to the sample creation page.

22 II. Entering a New Sample: Section 3 (Sample List)

23 II. Entering a New Sample: Section 3 (Sample List)

24 II. Entering a New Sample: Section 3 (Sample Creation Page)

25 II. Entering a New Sample: Section 3 (Sample Creation Page) Enter the sample name and a short description in the fields marked Sample Name and Sample Description. Select the source for the sample from the pull down menu. Click on the Submit button when you are finished. You will be taken back to the sample list page.

26 II. Entering a New Array: Section 4 (Array List) From the sample list page (or from the description page for your experiment, or the treatment list page), click on the Array List link in the footer. You will be taken to the array list page. Click on Create a New Array. You will be taken to the array creation page.

27 II. Entering a New Array: Section 4 (Array List)

28 II. Entering a New Array: Section 4 (Array List)

29 II. Entering a New Array: Section 4 (Array Creation Page)

30 II. Entering a New Array: Section 4 (Array Creation Page) Enter the array name and a short description in the fields marked Array Name and Array Description. Select the array type for the array from the pull down menu (Affymetrix, spotted array-cDNA, spotted array- oligo, other). Select the genus species and genotype used to make the array (the probe) from the pull down menus. This is the genus species spotted on the array itself, not the sample (source) hybridized to the array (target). Type in the strain used to make the array (if applicable). Again, this entry refers to the spots on the array and not the sample hybridized to the array.

31 II. Entering a New Array: Section 4 (Array Creation Page) Select the sample used to make the array from the pull down menu. This entry refers to the target hybridized to the array. Similarly, select the treatment used to make the array from the pull down menu. Enter the treatment time as text below. Enter a comment (excellent, good, slightly degraded, etc.) about the quality of the RNA extracted from the sample. Click on the Submit button when you are finished. You will be taken back to the array list page.

32 II. Entering a New Array: Section 4 (Array Creation Page)

33 II. Entering a New Array: Section 4 (Array Creation Page)

34 II. Entering a New Array: Section 4 (Array List Page)

35 II. Uploading Array Files (raw data) – Section 5 (Array List) From the array list page, click on the name of the array for which you wish to upload raw data files. You will be taken to the array display page. Click on Add New File To Array Array Name. You will be taken to the array file creation page. Click on the Browse button to locate the file on your hard disk or CD. Click on the Upload button to upload your file to the IMDS database.

36 II. Uploading Array Files (raw data) – Section 5 (Array Display)

37 II. Uploading Array Files (raw data) – Section 5 (Array File Creation)

38 II. Uploading Array Files (raw data) – Section 5 (Array File Creation)

39 II. Uploading Array Files (raw data) – Section 5 (Array Upload)

40 II. Uploading Analyzed Data Files – Section 6 (File List) From the description page for your experiment (or from the treatment list page, sample list page or array list page), click on the file list link on the footer. You will be taken to the experiment file list page. Click on Add New File To Experiment Experiment Name. You will be taken to the experiment file creation page.

41 II. Uploading Analyzed Data Files – Section 6 (File List)

42 II. Uploading Analyzed Data Files – Section 6 (Experiment File Creation)

43 II. Uploading Analyzed Data Files – Section 6 (Experiment File Creation)

44 II. Uploading Analyzed Data Files – Section 6 (Experiment Upload)

45 II. Uploading Other Experimental Files – Section 6 (File List) From the description page for your experiment (or from the treatment list page, sample list page or array list page), click on the file list link on the footer. You will be taken to the experiment file list page. Click on Add New File To Experiment Experiment Name. You will be taken to the experiment file creation page.

46 II. Uploading Other Experimental Files – Section 6 (File List)

47 II. Uploading Other Experimental Files – Section 6 (Experiment File Creation)

48 II. Uploading Other Experimental Files – Section 6 (Experiment File Creation)

49 II. Uploading Other Experimental Files – Section 6 (Experiment upload)

50 III. Searching for experiments Click on the Search Experiments link on the sidebar menu. You will be taken to the main search page. Click on the search criteria that you want to use. For this example, let us suppose that you would like to retrieve experiments that use a certain source. You would click on Source (Target). You would then be taken to the single search page, where you would chose from the sources in a drop down menu that represent the sources listed in the database. You would then click search to retrieve the results.

51 III. Searching for experiments

52 III. Searching for experiments

53 III. Searching for experiments

54 III. Searching for experiments

55 III. Searching for experiments

56 III. Searching for experiments The results page returns the following information about an experiment: experiment name, investigator, genomics site, starting date, experiment type, source (target), mutant name (target), strain (target), source /catalog number (target), genus species (target), genotype (target), ecotype (target), organ (target), tissue (target), treatment category, array type, genus species used to make array (probe), genotype used to make array (probe), strain used to make array (probe). Clicking on the experiment name takes you to the description page for that experiment. From this page, all information for the experiment can be accessed, including the download of raw array data and analyzed experimental data.

57 III. Searching for experiments

58 IV. Updating an experiment From either the experiment list page (accessed by clicking on the experiment list link in the sidebar menu) or through the search experiments function, you can locate a specific experiment to update. The description, treatment list, sample list, array list or file list can be updated for a given experiment by simply clicking on the parameter that you wish to update. You will be taken to a page that will display the current parameters and allow you to edit them. Finish by clicking on the update button.

59 V. Entering new sources Click on the source list link on the sidebar menu. You will be taken to the experiment list page. Click on Create a New Source. You will be taken to the source creation page.

60 V. Entering new sources

61 V. Entering new sources

62 V. Entering new sources

63 V. Entering new sources Enter the source name and a short description in the fields marked name and description. If applicable, enter mutant type, mutant name, strain and source/catalog number in the respective fields. If not applicable, enter N/A. Select the genus species, genotype, ecotype, organ and tissue from the pull down menus. Click on the Submit button when you are finished. You will be taken back to the source list page.

64 VI. Entering new treatment categories Click on the treatment categories link on the sidebar menu. You will be taken to the treatment list page. Click on Create a New Treatment Category. You will be taken to the treatment creation page.

65 VI. Entering new treatment categories

66 VI. Entering new treatment categories

67 VI. Entering new treatment categories

68 VI. Entering new treatment categories Enter the treatment category name and a short description in the fields marked name and description. Click on the Submit button when you are finished. You will be taken back to the treatment category list page.

69 VII. Reviewing the file access log. Click on the file access log link on the sidebar menu. You will be taken to the file access list page. The file access list page shows which user accessed the database (user name), whether the user wrote to or read from the database (access type), the date and time of access, and the accessed file name.

70 VII. Reviewing the file access log.

71 VII. Reviewing the file access log.