HELP
Viewing Gene Expression Data
The Marmoset gene Atlas offers the following ways for you to find gene
expression data:• Use Gene Search to locate a gene’s data by name, symbol, NCBI
accession number, or Entrez Gene ID. (2016 Apr)

Gene Search
Select age (neonate, 1-3 month, Young adult and Adult) of your interest. To
search for a specific gene by name, symbol, NCBI accession number, or Entrez
gene ID, type your query into the text box. As you type, genes that match yoursearch string will be suggested to you. Select an item from the list and click the"Search" icon. The results are displayed in a list that shows all genes withexpression data that match your query.

Gene Classification
The gene classification box lists the names of several human brain diseases.
When you select one of the diseases and click the search icon, it will display alist of ISH data of genes that have an association with the selected disease.
The information for gene-association of human brain diseases is collected byusing the Human–Mouse: Disease Connection (HMDC) in MGI(http://www.informatics.jax.org).

Dual Screen Image Viewer System
The experiment image viewer displays images for each selected ISH section in aviewer. You can zoom in by clicking (+) or by double clicking the location you
want to observe higher magnification. To zoom out, click the (-) button or
refreshicon. To observe a different section, scroll the bar under the
thumbnail images to the right to show more posterior sections and click thedesired thumbnail image to display a high-resolution image in the viewer. To
switch the screen to observe all sections, click theicon to switch thescreen. Once you select the image to show in the viewer, the corresponding
Reference Atlas section will be displayed side-by-side. You can move theposition of the section by dragging the image to the location you want to move to.
The reference atlas is synchronized to zoom in, or move with any action you
made on the ISH image. This view makes it easy to compare ISH data and theequivalent section of the Reference Atlas. You can also desynchronize the ISH
image and the Reference Atlas to compare different sections or differentpositions of sections by clicking the “Thumbnail Sync ON/OFF” icon and the“Image Sync ON/OFF” icon. You can download ISH images by clicking theicon. Select “current view” or “entire image” and download the image toyour computer.

Quantitative Expression Analysis
To quantify the average expression level of mRNA in different regions of theneonate marmoset brain, tissues from 17 regions were manually dissected from4 marmosets (7 regions from left/right hemisphere respectively (Fig), thalamus,
midbrain and cerebellum). mRNA were isolated using an mRNA isolation kit withthe manufacturer’s protocol and applied to Next-Generation Sequencing (NGS)
by Expression Analysis team (the Go lab). Data obtained from each sample
were analyzed and plotted by using RStudio software.

Fig. Approximate position of cortical region collected for NGS analysis.
Experimental Detail
Detailed information of each ISH experiment is shown in each window. The
primer sequence to isolate the target sequence and the entire sequence used togenerate the DIG-labeled probe is shown. The NCBI accession number is linked
to the NCBI web site.