Anatomy Transcriptomics
1. Go to the Brain Architecture - Cell Type - RNAseq portal. Click here.
This web portal can also be accessed through either
- the main Brain Architecture Portal by selecting in the top banner "DATA" -> "Mouse Cell Types" -> "Single Cell RNAseq".
or
- the Mouse Cell Types portal by selecting "Single Cell RNAseq" image.
All samples were sectioned coronally, registered post hoc, and displayed in the sequence of anterior (left) to posterior (right). There are several ways to navigate through the sections.
- Scroll through the film strip on the bottom of the page, showing coronal sections thumbnails. Clicking on individual section's thumbnail will bring the high resolution data to the main window.
- Click on the sagittal navigation tool on the lower right corner of the page. Clicking on a sagittal position of the brain will bring the closest coronal section to the main window.
We are constantly updating the anatomy data viewer with more informatics tools. Currently the following tools are steadily available:
- Atlas mapping. Clicking on "OVERLAY" will bring up the deformed atlas plane associated with the anatomy data. This algorithm was published in Tward et al. 2019.
The sample was sectioned at greater thickness (100 - 250 µm) and punched at various diameters (0.5 - 2 mm) for subsequent transcriptomics study. These sections with punches may appear with a tint or fragments due to the anatomical tissue processing.
For these sections, at the top banner, there is a link "snRNAseq data link". Click on the link will open up a new window showing the associated transcriptomics study at Single Cell Portal.
[9.Image highlighting the link.]
*[beta] Punch detection can be turned on by clicking "DETECTION" in the top banner. Clicking on the punches will bring you to the associated transcriptomics study at Single Cell Portal.
