Exploring the Human ABC Single Cell Atlas

Learn how to navigate the Allen Brain Map ABC Atlas to visualize cell types and marker genes. This guide helps researchers interact with complex spatial datasets to identify specific gene expression patterns within the brain.

Marissa Macchietto
40 steps
5 minutes

Brain-Map

Navigate to [https://brain-map.org/](https://brain-map.org/)

Click "atlases"

Click "Skip to main contentbrain knowledge platformatlasesour researchsupportBrain-map>AtlasesAtlasesHigh-resolution anatomical atlases with closely re..."

Click "Explore".

Switch to tab ABC Atlas"

Click "Skip to main contentbrain-map.orgBrowseExperimentExploreAnalyzeReferenceDevelopLoginSearchBrain Knowledge Platform>Explore>ABC AtlasABC AtlasThe..."

Click "Explore in ABC Atlas"

Click "Cell info (click for actions)Hippocampal CA1-3(Colored by 10x Whole human brain taxonomy (CCN20240330) › Supercluster)"

Click "Learn more"

Click "CA13_119"

Click "Marker Genes" to see top genes that define this cluster of cells.

Click "Add set to genes"

Click this icon.

Click this button.

Click "10x Whole human brain taxonomy (CCN20240…"

Click here.

Click "Supercluster"

Click this checkbox.

Click this icon.

Sort the neurotransmitters by the number of cells expressing the type of neurotransmitter. Because the UMAP is currently colored by "supercluster", we are able to see the proportion barplot showing the membership of the cells expressing a particular neurotransmitter type to each supercluster. \ \ Many possibly strange neurotransmitter combinations are winding up in the "splatter" cluster. Maybe these are real, or they could be multiplets.

Click on VGLUT2 to selectively highlight cells that express this neurotransmitter type on the UMAP. 190k cells express this neurotransmitter.

Click on VGLUT1 to selectively highlight cells that express this neurotransmitter type on the UMAP. 555k cells express this neurotransmitter.

Click the "Color By" button to color the cells by neurotransmitter type.

Now, we can see the breakdown of cells in each supercluster by neurotransmitter type. For example, the hippocampal CA1-3 is primarily the light blue neurotransmitter type (VGLUT1).

Let's view the cells of the deep-layer intratelenc. colored by neurotransmitter type.

Click "scatter brain container"

Now, let's color the cells on this UMAP visualization by the expression of the GFAP gene.

Click this icon.

Click "TRIP11"

Click this icon.

Click the "Search by gene symbol" field.

Type "GFAP"

Click "GFAP"

Click this icon to show the expression distribution across the selected UMAP.

Click on the "Color By" button to color the cells by GFAP expression.

The GFAP histogram is now colored by expression and corresponds to the cell colors in the UMAP.

Let's highlight part of the expression distribution to select the top highly expressed cells so that we can see where those appear on the UMAP.

Exploring the Human ABC Single Cell Atlas

Marissa Macchietto
40 steps
5 minutes

Brain-Map

Navigate to [https://brain-map.org/](https://brain-map.org/)

Click "atlases"

Click "Skip to main contentbrain knowledge platformatlasesour researchsupportBrain-map>AtlasesAtlasesHigh-resolution anatomical atlases with closely re..."

Click "Explore".

Switch to tab ABC Atlas"

Click "Skip to main contentbrain-map.orgBrowseExperimentExploreAnalyzeReferenceDevelopLoginSearchBrain Knowledge Platform>Explore>ABC AtlasABC AtlasThe..."

Click "Explore in ABC Atlas"

Click "Cell info (click for actions)Hippocampal CA1-3(Colored by 10x Whole human brain taxonomy (CCN20240330) › Supercluster)"

Click "Learn more"

Click "CA13_119"

Click "Marker Genes" to see top genes that define this cluster of cells.

Click "Add set to genes"

Click this icon.

Click this button.

Click "10x Whole human brain taxonomy (CCN20240…"

Click here.

Click "Supercluster"

Click this checkbox.

Click this icon.

Click on VGLUT2 to selectively highlight cells that express this neurotransmitter type on the UMAP. 190k cells express this neurotransmitter.

Click on VGLUT1 to selectively highlight cells that express this neurotransmitter type on the UMAP. 555k cells express this neurotransmitter.

Click the "Color By" button to color the cells by neurotransmitter type.

Now, we can see the breakdown of cells in each supercluster by neurotransmitter type. For example, the hippocampal CA1-3 is primarily the light blue neurotransmitter type (VGLUT1).

Let's view the cells of the deep-layer intratelenc. colored by neurotransmitter type.

Click "scatter brain container"

Now, let's color the cells on this UMAP visualization by the expression of the GFAP gene.

Click this icon.

Click "TRIP11"

Click this icon.

Click the "Search by gene symbol" field.

Type "GFAP"

Click "GFAP"

Click this icon to show the expression distribution across the selected UMAP.

Click on the "Color By" button to color the cells by GFAP expression.

The GFAP histogram is now colored by expression and corresponds to the cell colors in the UMAP.

Let's highlight part of the expression distribution to select the top highly expressed cells so that we can see where those appear on the UMAP.