GUDMAP Use Cases
- Within the testis, which structure expresses the gene Dppa5a (developmental pluripotency associated 5A)?
- What is the gene expression profile of Slc22a3 (solute carrier family 22) in the developing reproductive system?
- Which genes are expressed in the renal medullary interstitium, outer medullary interstitium and inner medullary interstitium?
- Is there a Leydig cell specific mouse strain? Name the reporter allele.
- How do you dissociate adult mouse Dorsal Root Ganglia (DRG) for Fluorescence-activated cell sorting (FACS)?
Within the testis, which structure expresses the gene Dppa5a (developmental pluripotency associated 5A)?
Step 1 On the home page of gudmap.org, use the search box and enter “Dppa5a” (or use Search > Gene in the top-level menu bar)
Step 2 Click the eye icon for the row in the search results:
Step 3 Scroll down to the “Specimens” table (or click “Specimens” in the right hand Contents sidebar) and hover over images to find results related to testis. Click the eye icon to view that record.
Step 4 Scroll down to the “Specimen Expression” table (or click “Specimen Expression” in the right hand Contents sidebar) and you’ll see that “primary sex cord” indicates expression is present but does not indicate a regional pattern.
What is the gene expression profile of Slc22a3 (solute carrier family 22) in the developing reproductive system?
Step 1 On the home page of gudmap.org, use the search box and enter “Slc22a3” (or use Search > Gene in the top-level menu bar)
Step 2 In the results, there are two rows for Slc22a3 - one for human data and one more mouse. The mouse dataset has an icon in the “Array Data” column that indicates there are microarray heatmaps available. Click the eye icon for that row.
Step 3 On the record page, scroll down to the Array Data table and you’ll see several heatmaps available by region.
Step 4 Look for the heatmap titled “Reproductive Gonadal”. You can hover over the bars to see the tissue sample titles. Red indicates more expression, blue indicates less expression.
Which genes are expressed in the renal medullary interstitium, outer medullary interstitium and inner medullary interstitium?
Step 1 From the homepage choose “Boolean Anatomy Search” in the Resources box. Or in the top-level menus choose Search > Boolean Anatomy Search.
Step 2 Set up a Boolean Query (you can find the help page here for more documentation). We will set up three different conditions - each for one of the anatomical regions where expression strength is present.
In the left hand section, in the search field above the tree, type “renal medullary interstitium”. When you see the term appear in the tree, click the term to populate the condition box on the right side.
Make sure the “Strength” field is set to “present”
Click the plus (+) sign to add another condition.
Repeat this step with the terms “outer medullary interstitium” and “inner medullary interstitium”. You should now have three condition on the right side of the screen:
Now click the “Search Specimen” button to search all gene records that show expression present in those regions:
In the search results, you’ll see in the Genes facet in the left sidebar the following genes: Crym, Wnt4, Ptch1
Is there a Leydig cell specific mouse strain? Name the reporter allele.
Click “Mouse Strain” link on homepage or choose Search > Cell & Animal Models > Mouse Strains in the main navigation menu.
In the search box above the search results, type Leydig. One result appears: Cyp11a1-GFP-Cre.
Click the eye icon to view the detail page for that strain.
Scroll down for the Mouse Strain Documents field and open the “Allele Verification” and “Allele Characterization” PDFs for more details.
In the characterization PDF, you’ll find that the allele
Cyp11a1-GFP-Cre is validated (needs verification).
How do you dissociate adult mouse Dorsal Root Ganglia (DRG) for Fluorescence-activated cell sorting (FACS)?
Click “Protocols” from the homepage or click “Search > Protocols” from the main navigation.
In the search bar above the main results, use keyword searches, such as: DRG FACS. You can also search through the Title and Keywords facets in the faceting sidebar.
Scroll through the results to find the protocol closest to what you’re looking for. Click the eye icon to view the record page.
You can scroll to view protocol steps on the page.
Or you can download the PDF version (in the “Original File” field):