How do I find out the total number of T cell epitopes reported for an organism of interest? How do I then determine the total number of CD4 versus CD8 epitopes?

• In the 'Search' interface on the left side of the IEDB home page, click the Organism Finder under the Epitope Source section to enter the source organism of interest. You can select from list of common selections (click on the selection and hit Apply Selection).
• If your organism is not in the list, type the genus/species under Find (Use NCBI taxonomy) and hit 'Search.' The Finder will locate your entry within the taxonomy tree and it will be highlighted in blue. Click on this and once the organism appears in the Current Selection box at the top, click Apply Selection.
• Back on the home page, go to the Immune Recognition Context section to include T cell Response (using the check box) by deselecting all other response types (default includes all four) and then hit 'Search' at the bottom of the page.
• This will generate a set of Search Result Summary tables of T cell epitope data only. The Search Result Summary table automatically includes additional information, including assay, reference, epitope source, immunized host and restricting MHC allele data. Click on the values in blue to display further details of the data.
• Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.

SIMPLE SEARCH for CD8/Class I or CD4/Class II epitopes:

• In order to further identify as specific subset of T cell epitopes within the broader set returned above, hit 'Revise Query' on the Search Result Summary page which will take you back to the Home page. Then, under the Immune Recognition Context section, select Class I (for CD8/Class I) from the pull-down list under MHC Class and then hit 'Search.'
• This will generate a set of Search Result Summary tables that includes all reported CD8/class I epitopes. For all CD4/class II epitopes, simply repeat the above process using Revise Search with the exception of selecting Class II.
• The Search Result Summary table automatically includes additional information, including assay, reference, epitope source, immunized host and restricting MHC allele data.
• Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.

ADVANCED QUERY for CD8 or CD4 epitopes (note that this will retrieve fewer epitopes for which recognition by CD4/CD8 cells has been explicitly shown):

• In order to specifically query for the number of CD8/Class I epitopes from an organism of interest, on the 'Search' pull-down tab along the top on the IEDB home page, go to T cell Search.
• Under Epitope, click the Organism Finder to enter the source organism of interest. Select from list of common selections (click on the selection and hit Apply Selection) or type in the genus/species under Find (Use NCBI taxonomy). Hit 'Search.'
• The Finder will locate your entry within the taxonomy tree and it will be highlighted in blue. Click on this and once the organism appears in the Current Selection box at the top, then click Apply Selection.
• Scroll down to the T cell Assay section, click on and expand the Effector Cell. Then, under Effector Cell Type, select T cell CD8+ (cell types are in alphabetical order in the menu). At the bottom of the page, click 'Search.'
• This will generate a set of Search Result Summary tables that includes all reported CD8/Class I epitopes.
• For all CD4/Class II epitopes, simply repeat the above process using Revise search with the exception of selecting T cell CD4+ under Effector Cell Type.
• The Search Result Summary table automatically includes additional information, including assay, reference, epitope source, immunized host and restricting MHC allele data.
• Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.