RID Help Manual

1. In Choose virus and subtype section
   • Step 1. Select a virus and a subtype or all subtypes of the virus in the “Choose Virus and Subtype” section.
   • Step 2. Select a host/genome build and a chromosome or all chromosomes in the “Choose Host and Chromosomes” section. To add options in the query, skip steps 3 and 4, and go to B).
   • Step 3. Select all attributes or specific attributes of integration sites in the “Integration Site Information Selection” section.
   • Step 4. Click the “Submit query” button.
   • Step 5. On the RID Query Result page, for each record, click the “I” button to display the provirus LTRs in the integrated host chromosome regions. Click the “G” button to map this site on the UCSC Genome Browser. Detailed gene information and the publication abstract will be displayed by clicking the gene_id hyperlink and pubmed_id hyperlink, respectively.
2. Query Options
   • In the “Enter an insertion site or a range separated by a comma” box, either type a specific nucleotide position to query the integration site at this position or enter a range of nucleotide positions to query all the integration sites in this range. A chromosome must be selected for this type of query.
   • In the “Enter a gene name” box, type a gene name to query integration sites in this gene. You do not need to select the chromosome where this gene is located.
   • Select “Check to view intergenic regions only” to query integration sites in the intergenic region only. This type of query works with either a specific chromosome selected or all chromosomes selected; it can also be combined with a PubMed ID to query intergenic sites in that publication.
   • Enter one or two PubMed IDs in the “Enter Pubmed ID(s)” box to query integration sites reported by the publication(s).
   • Enter one or two sample name(s) in the “Enter sample name(s)” box to query integration sites in the sample(s). Currently, sample names are derivatives of the PubMed ID. Sample names will be displayed by clicking the “Samples in RID” hyperlink.
   • Enter one or two tissue name(s) in the “Enter tissue name(s)” box to query integrations sites in the tissue(s). Tissue names will be displayed by clicking the “Tissues in RID” hyperlink.
   • Additional query options include tissue source (in vivo, in vitro, ex vivo), provirus orientation (+, -), ART treatment (yes, no), and viremic (yes, no). All the above query options can be combined.
   • The annotations of the integration sites from any particular publications can also be obtained by clicking the “A” button at DATA SOURCE tab.
3. Graphic Display of Integration Sites
   • To use “USCS genome mapping” and “Chromosome pattern plotting”, a single chromosome must be selected. More specifically, in “Queries Options” Section:
     • Enter a nucleotide position or range of positions to map the sites in the UCSC Genome Browser by clicking the “Genome mapping” button.
     • Enter a range of nucleotide positions to plot integration-site distribution on the selected chromosome by clicking the “Pattern plotting” button.
     • Enter a gene name to map the integration sites in this gene in the UCSC Genome Browser by clicking the “Genome mapping” button or plot the integration sites in this gene by clicking the “Pattern plotting” button.
     • Enter one PubMed ID in the “Enter PubMedID(s)” box to map the integration sites of the publication to in the UCSC Genome Browser or to plot the integration-site distribution by clicking the “Genome mapping” button or “Pattern plotting” button. Enter two PubMed IDs in the box to compare the difference in the integration-site mapping or distribution patterns of mapping or patterns of the integration sites between the two publications by clicking the “Genome mapping” button or “Pattern plotting” button.
     • Enter a sample name in the “Enter sample name(s)” box to map the integration sites in this sample in the UCSC Genome Browser or to plot its pattern. Enter two sample names in the box to compare the integration-site mapping and distribution patterns by clicking the “Genome mapping” button or “Pattern plotting” button.
     • Enter a tissue name in the “Enter tissue name(s)” box to map the integration sites of this tissue in the UCSC Genome Browser or to plot their distribution patterns by clicking the “Genome mapping” button or “Pattern plotting” button. Enter two tissue names in the box to compare the integration-site mapping and distribution patterns by clicking the “Genome mapping” button or “Pattern plotting” button.
   • To use “omicCircos genome plotting” to map integration sites to the host genome, all chromosomes must be selected. Users can enter one or two pubmed IDs in “Enter a pubmed id(s)” box, and then click “omicCircos genome plotting” button.
4. Advanced Queries

To find genes detected by multiple experiments, enter one PubMed ID in the “PubMed ID 1” box and another in the “Pubmed ID 2” box and click the “Genes detected by multiple experiments” box. If no PubMed ID is entered, the result shows genes detected by two or more studies.

If there are any questions, please contact Mary Kearney, Ph.D at rid@mail.nih.gov