How many genes will be done and in what time frame?

The Sleep Study project will complete a survey of 223 genes across 5 conditions, some with replicates, in 2007.

Will you make primers/clones available so that others can replicate the data?

The primer sequences and sequence IDs are available as metadata through the Sleep Study Web site.

What mouse strain are you using? Age? Sex?

C57BL/6J from The Jackson Laboratory. The animals are 8 week (56 days) old males. This strain of mice is the same as used in the creation of The Mouse Brain in Stereotaxic Coordinates by George Paxinos and Keith Franklin. This age/sex/strain is the same as used to generate the data for the Allen Brain Atlas project.

Where are the Nissl anatomical sections?

Nissl sections at 100 µm intervals within a specific tissue specimen are available. Click the "Show Nissl Image Preview" button in a thumbnail section's toolbar to view the corresponding Nissl images.

I see lines through many of the images at highest magnification, is data missing?

The Allen Institute has significantly improved image quality with respect to stitching image tiles together, but the stitching may occasionally be visible at high magnification.

Why aren't you using radioactivity?

Non-isotopic methodology was chosen because it allows the visualization of cellular morphology to a greater extent than radioactive measures. These methods produce a label that fills the cell body, in contrast to autoradiography that produces scattered silver grains surrounding each labeled cell.

What platforms and browsers are supported by the Sleep Study Web site?

Please refer to the Supported Platforms section of online help.

Why is there no link to the Allen Reference Atlas on the Sleep Study Web site?

The Allen Reference Atlas is maintained for the Allen Brain Atlas project. Please visit the ABA Web site to view it.

A gene I previously found on the Sleep Study Web site is no longer available. What happened to it?

Image series may be removed from the Web site to address quality concerns. You can expect the gene to be re-released if it was once available.

Are there restrictions on the use of the data? Will I be able to file for intellectual property on discoveries that I make using the data?

We encourage the use of the data for scientific discovery and research, subject to the Terms of Use.

How do I download an image file?

Open a thumbnail in the image viewer tool, click the "More Tools" button to display the context menu, then select "Download image as JPEG."

What is "expression level?"

Expression Level is calculated as the average signal intensity of expressing cells in a structure multiplied by the area occupied by signal in that structure. To allow cross-gene comparison, this number is normalized by the maximum possible cellular area, derived from the areal coverage observed for a set of ubiquitously expressed genes. For more information, refer to the Informatics Data Processing document.

What is "expression density?"

Expression Density is the ratio of the number of labeled cells in a structure to the total number of cells in that structure, derived from cell counts for a set of ubiquitously expressed genes. For more information, refer to the Informatics Data Processing document.

What is "expression pattern?"

Expression Pattern indicates whether a gene has a more "clustered" (non-uniform, regional) or "not clustered" (uniform, non-regional) pattern of expression in a given structure. Using methods of spatial statistics, the expression pattern is classified as being regional or uniform based on calculations of signal dispersion and uniformity. Genes exhibiting more uniform signal distribution are assigned to the class "non clustered," while genes having a more regional expression pattern are assigned to the class "clustered." The classification is made on a section by section basis, the results being averaged over all sections with expression in a given structure. For more information, refer to the Informatics Data Processing document.