Mouse V1 ALM RNA hub


This hub contains read pile-ups of single cell RNA sequencing data collected from the Visual cortex (V1) Anterolateral Motor cortex (ALM) of adult mouse. Details of this data set, along with links for download, exploration, and analysis can be found on the Allen Cell Types Database (see the "V1 & ALM - SMART-SEQ (2018)" ).

Useful links:

Browse tracks

Adjust configuration


This hub has single cell RNAseq data grouped into cell types at two levels of refinement. By default tracks of "subclass" are shown, which represent the average number of reads across multiple related cell types. The hub also contains separate aggregations for each individual cell type, which can be viewed as described below. These aggregations contain a random sampling of N=20 nuclei from that type (or all nuclei in the cell type if N<20). The aggregation tracks for subclass and cell type are normalized by counts per million (CPM).

UCSC Hub View:

By default all tracks for this hub will display using the same views and settings, which can be adjusted below. To return to default settings select "Reset to Defaults". To adjust the views for each track set BOTH the "Maximum display mode" and the "RNA-seq CPM" to the desired setting. If only one is set, the least restrictive of these settings is used for viewing (e.g., if one is set to full and the other to dense, the tracks will display as dense).

The "RNA-seq CPM Configuration" box includes a series of options for adjusting these views. The "Graph configuration help" button provides a lot more detail on each of these options. Most settings can likely be left at defaults, but if you want to change the track height, adjust the "max" value of the "Vertical viewing range" to a lower value. All tracks will be shown at the same scale, but will be capped at this max value in cases where tracks exceed the max.

The matrix view in the next box enables you to pick the specific subclass(s) or cell type(s) of interest for viewing and comparing reads. These can be added individually by selecting the appropriate radio box or in batch by column or row by selecting the approrpiate "+" or "-" button. You can also select or deselect tracks, as well as adjust the configuration of track individually using the list of tracks below.

Once you are happy with the settings, click "Submit" to explore. This will take you to the main page for browsing and gene search.

UCSC navigation and gene search:

To navigate to a specific genomic location, enter the gene symbol, genomic coordinates, or a related search term in the search box and click go. You can also navigate the local region by clicking and dragging the screen left or right inside the UCSC track box or by clicking the "move", "zoom in", and "zoom out" buttons on the top of the screen. Cell types and subclasses can be reordered within the display by clicking on the track name and dragging the track up or down. Finally to add external annotations tracks of interest, please pick from the multiple tabs in the main page screen which are available as you scroll down. You can return to the configuration page by clicking "V1 ALM composite expression" under the "V1 ALM RNA Hub" listed as the first tab.


Please post any questions you have to the Allen Brain Map Community Forum. Any topics or questions not covered in this file will be addressed on the community forum.