GENSAT

About

The Gene Expression Nervous System Atlas (GENSAT) is is one of the first large-scale efforts to look at where specific genes are expressed in the brain and spinal cord. The project is funded by the NIH's National Institute of Neurological Disorders and Stroke (NINDS).

The project focuses on two techniques:

• Evaluation of unmodified mice lines for expression of a given gene using radiolabelled riboprobes and in situ hybridization.
• Creation of transgenic mice lines containing a BAC construct that expresses a marker gene in the same environment as the native gene.

Designing gene-specific probes is an essential part of the GENSAT process. Before NCBI became involved in GENSAT's probe design, identifying a gene-specific region in the target was undertaken one gene at a time and involved several time-consuming manual steps. A different approach was therefore necessary to allow the project to be scaled up to process hundreds of genes per month.

NCBI automated the process of picking gene-specific probes using a rapid, multi-step process:

1. BLAST is used to identify regions of the target transcript that match a single location on the assembled mouse genome and also match mouse mRNAs from a single gene
2. segments of the target transcript that match repetitive or low-complexity sequence are excluded from consideration
3. primers are picked that will amplify 150-800 bp probes from gene-specific regions identified in the preceding steps
4. electronic PCR is used to check the specificity of the primers

This automated system can quickly design probes for a large batch of target genes and the primers selected succeed in amplifying the desired probe from cDNA preparation more often than primers selected manually

GENSAT organizations:

• Rockefeller University
• St. Jude Children's Research Hospital

Resources