How many genes will be done?
The Atlas project has completed a survey of approximately 20,000 genes.
What are you doing about alternate splicing?
The Atlas project's objective is to use one probe per gene. Probes are designed to be pan-specific for multiple transcripts of the same gene. Efforts are underway to develop shorter specific probes for detecting individual slicing variant.
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 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.
Why do some genes have both coronal and sagittal data sets, while others only have coronal?
Expression data for genes demonstrating particularly compelling specificity of expression are replicated at higher sampling density in the coronal plane of section that most neurobiologists and anatomists are familiar with.
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.
Why did you create another reference atlas?
The decision to construct in-house mouse brain atlases was made to correspond to the methodology of brain tissue preparation used for ABA in situ preparation. Additionally the reference atlas data hierarchy provides the common anatomical framework utilized during informatics processing in the ABA data pipeline.
What platforms and browsers are supported by this Web site?
Please refer to the "Supported Platforms" section of online help.
How do I use the Allen Reference Atlases when viewing a gene image?
The Allen Reference Atlases (ARAs) are brain atlases that provide an anatomic framework for brain regions, in both the sagittal and coronal planes, for the images you have selected. The ARAs are annotated using abbreviations to label the regions within the mouse brain. To view the ontology legend, click the quot;Show legendquot; button in the ABA Image Pane. When you select an ISH Image Pane, the relevant reference atlas automatically updates to the nearest corresponding reference atlas section.
How do I create a Boolean query?
Select the "Boolean Syntax Query" search option to create a custom query of the Brain Atlas database using specific field names and logical operators such as "and," "or," and "not." For details about the searchable database field names and the syntax required for Boolean queries, select the "Help" menu. Also see the link to query samples located above the query text box.
How do I search for more than one gene at a time?
The "Gene Search" text box allows you to search for genes by gene name, gene symbol, NCBI accession number, or Entrez gene ID. Search for more than one gene at a time by separating each of your search terms by a comma or space. Or, if you clicked the "Input Bulk Query" button, separate each search term by a line break. For more detailed search, select the "Help" menu.
How do I superimpose gene images?
To superimpose images, drag the Image Pane title bar until the image snaps on top of another Image Pane. You can adjust each image individually in order to allow the underlying background image to show through for better comparison (each image contains Color Controls). Please access our "Help" tab for more detailed instructions.
Can I link to information from other data and publication sources while viewing a gene image?
Yes, please access the metadata section located in the results table or above the images in the thumbnail view and click the active links. Or, you can access the metadata from the Image Viewer by clicking on the information button within the Image Pane.
The image viewer is freezing or behaving erratically. How do I adjust it?
Use the "Restart Viewer" button located in the upper right section of the viewer.
If there are additional features that would enhance my experience with the ABA, how do I submit my request?
If you have suggestions for how we can improve the ABA Application please submit your comments through the "Contact Us" link located at the bottom of each page.
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.
Is it possible to download the data in a batch form? Is programmatic access to the data possible?
Programmatic access to images, experiment metadata, and informatics annotations is made available through an application programming interface (API). Click "API" on the navigation bar to learn more.
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.