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SEARCHING THE IN SITU

HTML
 

HYBRIDIZATION (ISH) DATA

Table of Contents
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classtoc-style

Gene Search

To search for a specific gene or group of genes, type its gene name, gene sympol, NCBI Accession number, or Entrez Gene ID into the search box. Make sure the Gene radio button is selected 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 three or more letters in its name or symbol and appending an asterisk ( * ) as a wildcard. You can also browse through the genes by clicking on a category.

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You can sort the search results or further refine your query using the #Advanced Advanced Search feature.

Advanced Search

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The following special operators can be used to build queries:

Operator

Example Search Type

Example Query

AND operator: &

Gene

dopamine & receptor

OR operator: |

Gene

ABAT|ACHE

NOT operator: !

Gene

"dopamine receptor" !DRD3

  • AND, OR and NOT may be used in place of their corresponding operators. They must be upper case.
  • The AND operator (&) is implicit, so spaces between words that are not separated by an operator will be treated like an &.
  • OR (|) has higher operator precedence than AND (&).
  • Parenthesis can be used to group criteria, but nested parenthesis are not supported at this time.
  • The NOT operator (!) is not supported within parenthesis.
  • Enclose search terms in quotation marks to avoid confusion with boolean operators. For example, hyphenated words should be enclosed in quotation marks (i.e. "ATP-binding").

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Based on your search criteria, a list of experiments will be returned as described in the table below. Search results can be sorted by up to three categories indicated by the drop down menus. Search categories are prioritized from left to right and include all searchable columns. The checkbox labeled "asc" (ascending order)indicates the sorting direction for each column, so when checked, the sort progresses from a to z , or 1 to n, depending on whether the column is alphabetic or numeric. Leaving the box unchecked sorts the column in descending order, that is z to a, or n to 1.

Column

Description

Image Modified

Add the image series to your selections by clicking a checkbox. The selected series can be opened in the Zoom and Pan Image Viewer by clicking, "View Selections"

Experiment ID

Click the ID to view an

#Experiment

Experiment Details Page

Gene Symbol

Click on symbol to view a

#Gene

Gene Details Page

Gene Name

Full gene name

Tissue Location

Specimen origin

Age

Donor age

Sex

Male/Female

Donor

Allen Institute donor ID

Related Data

Click the "Related Data" button to display a list of Allen Brain Atlas resources for the species indicated. Please note that the current project is excluded from the list of suggestions. For example, if a "human" link is displayed while viewing human microarray data, it refers to related ISH data.

ISH - Image Viewing

The Zoom and Pan (ZAP) Image Viewer window allows you to view the images from one or more experiments once they have been selected from the search returns list (by clicking the checkbox(es) and clicking "View Selections"). Each ZAP viewer consists of a filmstrip of thumbnails - which when selected will bring up the image in the main viewer, tools to navigate the image in the main viewer and a scale bar to determine the approximate size of the area in the main viewer.

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Thumbnails for the entire image series are displayed across the bottom of the viewer in section order. Click a thumbnail to select it for viewing, or use the keyboard to navigate through the set. The current selection is outlined in black.

Toolbar

Icon

Description

Image Modified

Move the slider bar to the left to intensify the contrast or color

Image Modified

Show current image in a full-screen viewer with

#side

side by side Nissl comparison

Image Modified

See the images series in contact sheet format

Image Modified

Select ISH, Nissl, or Expression image type

Image Modified

Open a new window to view the image series' details

Image Modified

Close the current viewer

Scale Bar

Shows the current viewing resolution of the image, in microns. This value dynamically changes as you zoom in/out of the image. You can position the scale bar anywhere on the main image by dragging the scale bar by its ruler.

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Once you click on the full screen viewer button, you will be taken to a screen with side by side viewers. The left hand viewer shows the ISH image series and the right hand viewer displays the closest Nissl image from the same specimen block. Clicking on another ISH image will automatically display its nearest Nissl section. Clicking on an image thumbnail in the Nissl image series will automatically take you to the nearest ISH image. While the "Sync" box is checked the Zoom and Pan functions will affect both images. Round spots on the Nissl image are "hotspots" and when hovered over will display the name of the structure. Clicking on the hotspots while viewing ISH images from an adult brain will take you to the Adult Human ISH Guide. While viewing pre-natal ISH images, clicking on the hotspot will take you to the appropriate aged prenatal Reference Atlas.

Keyboard Commands

Key

Description

F

Advance to the next image in the series

D

Go back to the previous image

R

Advance to the last image in the series

E

Go back to the first image in the series

A

Zoom in

Z

Zoom out

Expression Mask Colors

The Expression Mask image display highlights those cells that have the highest probability of gene expression using a heat map color scale (from low/blue to high/red).

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Clicking on the specimen link from the search results page or on the specimen link in the experiment details page will take you to detailed specimen information. Specimen detail information includes Specimen Information, #Specimen Specimen Block Layout, #Section Section Information, #Gene Gene Information and an #Image Image Viewer.

Donor/Specimen Metadata

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The section information box lists information from the current gene pictured in the image viewer including the gene name, the experiment ID, the section number, the treatment and which study the data came from.

 

 

Gene Information

The Gene information section lists the genes that were assayed in this specimen block.

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