Finding your Assay with the Available Genome Sequence Information
SABiosciences is currently using the following NCBI Genome Build Versions:
Human Genome Build: 36 Version: 2
Mouse Genome Build: 36 Version: 1
Rat Genome Build:4 Version: 1
The Chromosome RefSeq Version number used to define your chromosomal position may be different from the Chromosome RefSeq Version number in the Genome Build currently used by our database. The different version numbers will very likely have different chromosomal position numbers for the same sequence. To convert chromosomal positions between versions, use the NCBI's BLAST algorithm to find the sequence from the version number used in our database, specified above, that matches with the available sequence from your version number information.

Assay Description:
SABiosciences designs ChIP-qPCR Primer Assays at roughly 1-kb tiling intervals about every human, mouse, and rat promoter in a 30-kb range from -20 kb to +10 kb relative to each RefSeq transcription start site (TSS). Assay nomenclature includes the dominate NCBI Gene Symbol and TSS specifying RefSeq Accession number plus the tile number. Tile numbers refer to the boundary furthest from the TSS. For example, a "-03" tile refers to the -2000 to -3000 bp range; a "+03" tile refers to the +2000 to +3000 bp range.

Finding the closest assay(s) to your chromosomal position
Because ChIP-qPCR Assays fall anywhere within a specified 1 kb tile region, the closest assay to your binding site may actually lie in an adjacent tile. Therefore, check the assay index positions of the adjacent tiles for their proximity to your ChIP target site. Also, more than one assay may be located within 1 kb of the chosen position or binding site and, in this case, try both assays to find the one that provides the best response or to get complementary or confirmatory data.

When searching for a specific Chromosomal Position, the database will return the assay with the index position closest to and within 1 kb of that position, if possible. However, your Chromosomal Position of interest may not be within the 30 kb tiling range of a known or predicted promoter. In such a case, the search engine will return a null result and suggest the reason.

A ChIP-qPCR assay may be designed to a non-promoter region using our Custom ChIP-qPCR Assay Design Service. For more information, see our Custom ChIP-qPCR Assays web page or contact one of our Application Specialists by phone at 888-503-3187 or by email at support@sabiosciences.com.

Availability of Assays:

Pre-Designed Versus On-Demand: A growing number of popular promoter regions have been automatically pre-designed and populated into the database driving this search engine. Other assays are designed on-demand with a two business day turnaround time. To request an assay design, simply provide your contact information when prompted. We will notify you of the results once they are available.

Missing Assays: Assays for some tiles cannot be designed with our default design parameters due to innate sequence characteristics within the relevant 1 kb tile region (for example: repetitive elements, low sequence complexity, high GC content, etc.).

Failed Assays: Once a designed assay is ordered, the assay still needs to pass rigorous quality control standards after production including a real-time PCR run. In rare cases, assays fail quality control prompting an automatic re-design of the tiling assay primers.

For missing or failed assays: We will immediately contact you to help you examine the available options for your target site of interest. We may recommend assay re-design, the use of adjacent tiling assays, or our Custom ChIP-qPCR Assay Design Service. For more information on our Custom ChIP-qPCR Assays, contact one of our Application Specialists by phone at 888-503-3187 or by email at support@sabiosciences.com.

Return to the ChIP-qPCR Assay Search.