Project data is available as colorimetric in situ hybridization (ISH) and Nissl images. Images are grouped into image series that comprise an experiment. Experiments consist of slides from the same specimen that receive the same treatment, whether it is Nissl staining or ISH with a probe for a particular gene.
You can search for a gene using its gene symbol, name, or Entrez gene ID. First, select the "Gene" radio button, type the search term in the input box above the ISH Data window and click the "Search" button. You will be offered suggestions to choose from while you type, but you can also search by typing the first few letters in its name or symbol and appending an asterisk ( * ) as a wildcard. Note that to use an image series ID for search, you will need to use the "Advanced" search feature. From the "Data" tab, you can browse for a gene by either choosing the first letter in its gene symbol or click on "All Genes."
| Category | Values |
|---|---|
| gene symbol | i.e. Prox1 |
| i.e. A230003G05Rik | |
| i.e. prospero-related homeobox 1 | |
| i.e. 19130 |
Select the "Anatomic" radio button to search for genes that are predominantly enriched within the selected brain structure. Results will be returned for the specified age. Image series are ranked by the specificity of the gene in the brain structure of interest as opposed to adjacent brain regions. Thirteen structures are generally available for search for each age, with the exception of E11.5, for which five structures are available. The results are provided as a list of individual image series (experiments) for the given age and search query.
Please refer to the Informatics Data Processing white paper for additional details.
Select the "Temporal" radio button to search for genes that are enriched at a specific age within the selected structure. Note that this feature does not search for spatial enrichment; Anatomic Search should be used for that purpose. This search feature compares gene expression in the given structure at the given age and compares it to expression in the same structure at 7 other time points. Genes are ranked by their temporal enrichment in descending order, with the most temporally enriched genes first. Because this feature requires the comparison of data across ages, the search results are grouped by gene, not image series.
Please refer to the Informatics Data Processing white paper for additional details.
Additional search terms can be used to narrow a gene search using the "Advanced" radio button. The categories that can be selected for search are:
| Category | Values |
|---|---|
| age | E18.5, E15.5, E13.5, E11.5, P4, P14, P28, P56 |
| sagittal, coronal | |
| i.e. 100020260 | |
| i.e. NM_008937 |
Furthermore, Boolean Syntax can be used in the search box to craft a specific query.
The following special operators can be used to build queries:
| Operator | Example Search Type | Example Query |
|---|---|---|
| AND operator: & | Gene | glutamic & acid |
| OR operator: | | Gene | Abcc1 | Ache | Adcyap1 |
| NOT operator: - | Gene | Grik* - Grik2 |
Neuroblast searches for image series that have similar expression to the image series and structure specified.
There are two ways to initiate a Neuroblast search:
If you do not already have an Allen Institute image series ID for your gene of interest, use one of the other search options to find an image series. Each image series has a list of "Neuroblast structures" that can be used to initiate a Neuroblast. You can either search for genes similar to the target gene in a specific brain region or for the whole brain (neural plate).
Please note that the Gene, Advanced, and Temporal searches group the search results by gene. You may need to click the " + " button to show the list of image series associated with the gene.
Once you have selected a structure from the Neuroblast list for an image series, the list of resulting image series will show up, ranked in order of similarity to the selected image series for the structure specified. The gene symbol and ID associated with the selected image series, as well as the selected structure's name will be displayed above the search results.
Please refer to the Informatics Data Processing white paper for additional details.
Gene searches return a list of genes that match your search criteria. Image Series Metadata searches return a list of image series that match your search criteria grouped by gene. The gene search result columns include the following:
| Column | Description |
|---|---|
| Click the show button (+) to expand the image series associated with the gene. Click the hide button (-) to collapse the image series section. | |
| Full gene name. | |
| Click the gene symbol to open a new window with additional gene metadata. | |
| Accession number | |
| Links to related data on Allen Institute project Web sites. |
The following columns are displayed when the Image Series section is expanded:
| Column | Description |
|---|---|
| Add the image series to "Your Selections.". The selected image series can be opened in the Zoom and Pan Image Viewer by clicking the "View Detailed Images" button, or you can view their metadata by clicking "View Selection Details." | |
| Click the link to open a new window with metadata for the image series. | |
| Embryonic (E) or Post Natal (P) age. | |
| "sagittal" or "coronal." | |
| Probe orientation with values of "sense" or "antisense." |