Compare our Visium HD dataset with 10X sample ms brain

Collaborative Work Between Qiu and DAI lab, UA COM-Phoenix

Our dataset is has much higher quality than the 10X Genomics sample mouse brain dataset (FFPE section).

This is a low resolution image of the 10X Genomics sample dataset, with unsupervised clustering mouse cortex and hippocampus.

Zoom in view of cortex region. Note alignment issues, and swollen soma, nuclei, HE staining artifacts in the image.

Comparison of our own sample:

unsupervised clustering

Detecting Pvalb gene expressing spot on 10X sample dataset, most spots are not centered on soma region:

Pvalb-expressing neurons of our own sample: Note detected UMI is highest around soma, but also present within the local dendritic arbor regions of Pvalb neuron!! This is truly amazing…

Pvalb PFC cells

Web Summary of the 10X mouse brain FFPE section dataset

Unsupervised clustering of 10x dataset:

Our own dataset, note ~3X detected transcripts number per spot.