It's really simple. Just click on Search and confine your search in the form by choosing one of the available applications, organisms or detection chemistries. More specifically, you can search for a gene symbol/name, Gene ID and/or NCBI reference SNP cluster ID (rs#), PubMed ID from an article in which the primer sequences are described, primer/probe sequence, group name or submitter's name. If available suggestions will be supplied, you select the desired suggestion by clicking on it. If you want to order your search results, choose one of the possibilities in the Order By field.
Alternatively, you can perform a quick search on the homepage. Here, you can only search by gene name or gene symbol or by RTPrimerDB ID. It's possible to restrict the search to one organism. Press click Search to send your request and obtain the search results.
It's also possible to add filter settings by clicking on Change search filter settings on the search page. The filter can speed up your search by setting default settings for specific search options such as for example organism, applications and detection method. Let's say you are only interested in human assays. Instead of specifying the desired organism each time you want to perfor a search, you can go to the filter page and supply the desired organism there in the corresponding filter option. After saving and turning the filter on (if the filter has been turned on a filter symbol will appear next to the search menu : ), this organism will now be included in every search you perform. So you don't need to specify the organism of interest anymore.
Alternatively, you can browse for an assay. On the Browse page, you click on the organism of interest (step 1). In step 2a all the genes are grouped by their first letter and visualized as an alphabet. Clicking on a certain letter will give you a list of all the genes starting with this letter. In the gene list you can click on the gene symbol itself to visualize all the assays corresponding to this gene. It's also possible to restrict this search to a specific application by clicking on the desired application (on the right side of the gene symbol). The number inside the rectangle indicates the number of assays correspondig with this gene and application. Finally, you can visualize all the reference genes of the selected organism by clicking on Show all reference genes at step 2b.
Searching a publication is almost identical to searching an assay. First select the publication radio button to go the the publication-search page. In the same way as for search an assay, multiple options (author, journal, publication year, ...) can be used to restrict your search.
Browsing for a publication can be done as well. Go to the Browse page and select the publication radio button to go the the publication-browse page. Step 1 will group all the words of all the publications according to their first letter, this will again be visualized as an alphabet. Clicking on a certain letter will give you all the title-words starting with this letter followed by the number of assay associated with this letter. Clicking on this number results in the visualization of all the publication(-titles) in which the selected word is present and again the number of assays, this time grouped per application. Clicking on the publication title will guide you to the associated publication report containing additional information about the publication, while clicking on a application will show you all the corresponding assays (the number in the black box is the number of genes associated with this publication, clicking this will show you all the assays over all the applications).
Step 1 : Selection of the application and the detection method. The information needed to be supplied during the following steps will be different, depending on these two selections.
Step 2 : Selection of the organism and gene. The method of selection is identical as for querying the database, suggestions will be shown and a suggestion can be selected by clicking on it.
Step 3 : In this step the oligo information needs to be supplied. Depending on the selections in step 1, the sequence of one or more forward primers, reverse primers and probes will have to be entered. If necessary, 3' and/or 5' will have to be submitted as well. The annealingstemperature is mandatory since this value will be used for the secundary structure analysis based on UNAfold. Entering the amplicon length is optional.
Step 4 : This is an optional step to include some experimental data of the assay. If an identical assay is already present in the database, this experimental information will be linked to the existing assay (no new assay will be created).
Step 5 : The last step of the submission process is also optional and can be used to associate the assay to a publication. When supplying a PubMED ID, the information of the corresponding publication (title, authors, abstract, ...) will automatically be retrieved from PubMed, a publication will be created (if it does not already exist) and the assay will be linked to this publication. If an identical assay is already present in the database, the publication will be linked to the existing assay (no new assay will be created).
If you need to upload a lot of assays, you can use the Large dataset submission template available on the Index > Downloads page to send your assays to us. We will then upload your assays in batch.
Performing an insilico evaluation can be interesting since it gives you the possibility to see the genomic region in which your assay is located. To perform such an analysis, first an organism has to be selected (the selection method is identical to the one used for searching and submitting an assay). After selection of an organism, the field for selecting a gene symbol will become available. In addition to these to fields, the fields for the forward and reverse primers, the template (cDNA or DNA) and the annealingtemperature are mandatory as well. The annealing temperature will be used to perform a secundary structure analysis based on UNAfold. The fields for the probes are optional and can be used to supply the sequence of your probe(s) if necessary. If all the information has been submitted correctly, clicking Evaluate will start the insilico evaluation.
On the evaluation results page, information about the gene and organism is shown on top. If the scripts was able to perform a successful alignment, this alignment will be shown on the bottom of the page. Buttons to perform a NCBI Blast, UCSC PCR, Bisearch search and/or UNAfold secondairy structure analysis, will be visualized if applicable.
The registration page can be reached in two ways. If you haven't logged in yet, clicking on Log in in the upper right corner of any page, will lead you to the login page where there is a link to the registration page : You can register here. Also, in the menu on the left under the My account header, you can see a Register topic among others. Clicking on this topic will also redirect you to the registration page. After registration you will receive a confirmation email with a temporary password which you will have to change first to activate your account and be able to login. Under the same My account header you can also see a Change password, a
What is a group? A group can be seen as a group of people having something in common, for example all the people working in the same lab or working on the same project. For example, you want to organize/group all the primer pairs or assays used in your lab (or present in your lab). In this case you could create a group having as name the name of your lab and invite all your lab-colleagues to the group (your colleagues will have to be registered in RTPrimerDB in order to be able to do this). Now you can also link all the assays used in the lab to the newly created group, making it easy to view, browse through or search in all these assays by just a few clicks. In this way such a group could be used as primer/assay database for your group.
To create a group, first go to the My account page. In the menu on the left side of this page, you can see the header My groups. If you are already member of one or more groups, this page will show you some details of the groups and offers you the opportunity to unscribe from a certain group by clicking on the Unscribe link next to the group name. Clicking on the icon, will bring you to the page where you can subscribe to a group or create a new group. If the group you want to subscribe to already exists, just select the group from the dropdown box and click on Subscribe. Your group application will then be send to the administrator of that group who can reject or accept it. On the same page a new group can be created by filling in the form. You need to designate who will be the contact person or administrator of the group (this person needs to be registered in RTPrimerDB).
If you are the contact person of one or more groups, a icon will appear in the upper right corner of the My groups page. By clicking on this icon you will go to the group-administration page where the group applications are shown (clicking on grant or deny will give that person access or not to the group). In the bottom half of this page you can see the groups you're a member of, clicking on the group name will guide you to the details page of the group while you can use the View assays link to visualize all the assays associated to this group.
Adding an assay to a certain group is easy. Go the assay you want to add to a group and click on the icon. On the next page you will see all the groups you're a member of, preceded by a or a symbol. Clicking on the symbol will add the assay to the corresponding group, clicking on the symbol will delete the assay from the group. If you're the contact person of a group, there is an additional way to delete assays from this group. By clicking on the View assays link of a group on the group-administration page, a list of all the assays associated with that group will be shown. There you again can delete an assay from this group by clicking on the symbol.
To creat a publication, go to My account and click on the My publications topic in the menu on the left. A page will appear with a icon in the right top corner. Clicking on this icon will move you to a page where you can create a publication by entering the PubMED ID of the publication/paper. Submission of a PubMED ID will also result in the retrieval of all the information of this paper from PubMED. If you get the message that the publication already exists, but you don't have access to it, it means someone else already created this publication and only that person can add/remove assays to/from this publication.
Adding an assay to a publication can be done on the My publication page (see Q8). On this page you can select a publication from th dropdown list to view all its assays. All the assays which have not been orgnanized in other publication-subgroups yet, can be found under All the assays of this publication. To add additional assays to a publication click on the Add assay link next to the All the assays of this publication header, select the desired assays using the checkboxes on the next page and click on Add assay(s). In a publication extra subgroups can be greated to organize the assays, a subgroup Reference is automatically generated when creating a publication (The Reference subgroup can be used to group all the assays of the publication which have been used as reference-assays/reference genes. The assays in this subgroup will be visualized when querying for reference-assays in the Search or Browse page). New subgroups can be created by clicking on Create a new group. Assays can be assigned or deleted from a certain subgroup using the Add assay and Delete assay links next to the subgroup header of the assay.