Welcome to ProbeDB!

The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.

As of February 19th, there were almost 10,000,000 records in the probe database. These records cover experimental applications such as Genotyping, Gene Expression, Gene Silencing, Variation Analysis, and Genome Mapping. Records are available for a wide variety of probe technologies.

NCBI ProbeDB is integrated into NCBI Entrez. This allows the user to search Probe DB like other databases in the NCBI family such as PubMed, Nucleotide, GEO, UniGene, dbGaP, and OMIM (among others). These databases allow users to incorporate advanced search options such as Limits, Index/Preview and History to give maximum flexibility while searching and offer users an effective way to drill down for records which will be most helpful to their specific needs. They are described in detail on other NCBI’s help pages: see PubMed or OMIM help documents for good examples.

ProbeDB offers fantastic resources to the user community:

Basic, well-illustrated tutorials are available by clicking on the links listed on the left-hand bar throughout the Probe Database. These short descriptions of different probe technologies, their uses in research and medicine, and brief synopses of large-scale projects based on probe-generated data are in the public domain for users to download and distribute freely.

Probe DB allows you to find known RNAi reagents for a specific gene.

For example: I’d like to find out what RNAi reagents are available for the human gene GRPR (gastrin releasing peptide receptor).

Step By Step Guide

1. Open NCBI Probe database

Fyi/note: The link above takes you directly to the Probe database. However, if you start from the NCBI home page, you can get to Probe by selecting that database from the Search pop-up menu near the top of the page, then pressing the “Go” button (or select “Probe” from the Entrez home page, i.e., global query page).

1. Use “Preview/Index” to see list of available parameters – italicized one-sentence summary of what you do in this resource or step

• In the lower text box of the Preview/Index page, select “Organism” from the search field pop-up menu
• Press the Index button to see a window on the index and browse the available organisms, which are listed alphabetically
• Select the organism(s)of interest. If you want to select more than one, use the CTRL key along with your mouse
• Use the AND button to pop your selected terms up into the text box at the top of the page, which shows your active query
• In the same popup menu box, select Gene Name and type GRPR into the text box
• Use the AND button to pop your selected terms up into the text box at the top of the page, which shows your active query
• Press Go button to retrieve the records (or the Preview button to first see how many records are retrieved, then you can press the number of records to view them)

1. Construct a specific search query

• For example, searching “GRPR[gene name] AND Homo sapiens[organism] AND trc[project]” in the probe database would return all reagents for GRPR in humans which have been submitted by the RNAi Consortium (trc)