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Vol 14 No 1 of NCBI News

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In this issue

GENSAT Project Data Now in Entrez


Influenza Virus Resource

NCBI ToolKit Utility Programs

New Microbial Genomes in GenBank

Iceman Preserved in GenBank

RefSeq Updates

RefSeq Release 11

New Organisms in UniGene

GenBank Release 147

New Genome Build

CCDS Database

NCBI Courses

PubMed Corrects Spelling


LocusLink Retired



GENSAT Project Data Now in Entrez


The Gene Expression Nervous Systems ATlas (GENSAT) provides the anatomical location of gene expression in the mouse brain GENSAT is based on BAC transgenic vectors in which endogenous protein coding sequences have been replaced by sequences encoding a reporter gene (EGFP). The EGFP is visualized in these sections by staining with an anti-EGFP antibody, or by confocal microscopy of unstained tissue sections. The images show the relative rates of transcription for each target gene. Images are available for mice at embryonic day 15.5 (E15.5), postnatal day 7 (P7) and adult developmental stages. In addition, GENSAT contains images taken at various developmental stages of tissue sections from non-transgenic mice lines in which the expression of a given gene is visualized using radiolabelled riboprobes with in situ hybridization.

GENSAT can be queried by gene name, alias or symbol, region of brain, imaging methods such as in situ hybridization, or confocal microscopy, section types such as saggital, horizontal, or coronal, and the age and sex of the mice. As with all other Entrez databases search terms can field-limited and combined using Boolean logic. For example, we can use the following query to get a list of images for genes with localized expression patterns:

“region specific”[Expression Pattern] AND “strong”[Expression Level] AND “neuron”[Cell Type]

Here, we are using the standard Entrez syntax to search GENSAT for the phrase “region specific” within the field “Expression Pattern”, indicated within the square brackets, combined using boolean “AND”s with two other field-limited phrases. Such queries can be built easily with the tools available in the Entrez “Preview/Index” tab visible in Figure 1A. The search returns summaries of image sets for over 5,000 genes as shown in Figure 1.

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Click on image to view larger

Figure 1: Entrez summary of GENSAT records matching the query given in the text. Clicking on the thumbnail image for the first record in "A" generates the view in "B" showing details of the set of images for serotonin receptor 4 and links to other Entrez databases in the "Links" menu.

The summaries include a zoomable, thumbnail size image of the brain section, seen in Figure 1A, the total number of images that are available for each image type, and the stage of development. Double-clicking on the thumbnail image for the first image set, that for 5-hydroxytryptamine receptor 4 (serotonin receptor 4), generates a more detailed report shown in Figure 1B. Links to other Entrez databases, including Entrez Gene, Nucleotide and PubMed, are provided within the “Links” menu. To open the image browser, click on the image of Figure 1B or the cropping icon, visible under the Links menu. The image browser, Figure 2A, can be used to select, magnify and simultaneously display up to 30 subsections of the original image.

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Click on image to view larger

Figure 2 : GENSAT image browsing tool. The rectangular area in "A" is used to zoom to the detailed view in "B" showing the expression of the dopamine 4 receptor as dark EGFP density in the elongated axons of neurons. Controls for viewing successive images in the set are visible in the lower right of the figure.

The GENSAT project, is an ongoing, collaborative study between the Rockefeller University and the St. Jude Children’s Research Hospital, and aims to map the expression of genes in the central nervous system of the mouse during the normal development. GENSAT is supported by a grant from the National Institute of Neurological Disorders and Stroke (NINDS) to the Rockefeller University. The data from this study will shed light on the genetics of disorders that affect the central nervous system and also provide insight into the brain’s response to both natural and foreign chemicals.

A list of the genes examined in this study can be obtained by searching Entrez Gene with the query:

“gene_gensat” [Filter]

The modified mouse lines are being deposited in the Mutant Mouse Regional Resource Center (MMRRC).

The image data and supplemental information from the GENSAT project can be downloaded from:

Details on the experimental methods and results of the GENSAT project are published in Nature. 2003 Oct 30;425(6961):917-25.

The data in the GENSAT database can be accessed by searching from the GENSAT home page at:

or from within Entrez at:

Questions regarding GENSAT should be sent to:


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