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Title: Spatially resolved transcriptomics reveals unique gene signatures associated with human temporal cortical architecture and Alzheimer's pathology.

Authors: Shuo Chen^†, Yuzhou Chang^†, Liangping Li, Diana Acosta, Cody Morrison, Cankun Wang, Dominic Julian, Mark E. Hester, Geidy E. Serrano, Thomas G. Beach, Qin Ma^$, Hongjun Fu^$

Abstract: bioRxiv

Code: Download

Sample 1

Name: CT-1

Loupe file: Download (1.27 GB)

Sample 2

Name: CT-2

Loupe file: Download (1.31 GB)

Sample 3

Name: AD-1

Loupe file: Download (1.06 GB)

Sample 4

Name: AD-2

Loupe file: Download (1.45 GB)

Unsupervised clustering

Clustering results for four samples are displayed based on Seurat integration method.

Manual annotation

Spatial maps of the eight clusters for each individual sample from manual annotation.

Circos plot

Circos plots of the connectivity strength within and across modules for ST spots in control (CT) human MTG, and with specific AD pathologies (Aβ, AT8, Aβ/AT8, GFAP/Aβ/AT8, and P2RY12/Aβ/AT8).

Circos plots are composed of four different modules M1-4 (top 15 hub genes each module); nodes which represent highly deregulated genes from each module; and edges (green lines) which indicate degrees of co-expression (high: dark green, low: light green).

Module score

Public available 10x Visium ST data and Kristen R. Maynard' paper (PMID: 33558695 ) of the human frontal cortex is annotated by our layer-specific marker genes.

Heatmap

Heatmap of Z-scores for upregulated and downregulated differentially expressed genes (DEGs) specific to ST spots localized with and without different AD pathologies (Aβ, AT8, Aβ/AT8, GFAP/Aβ/AT8, and P2RY12/Aβ/AT8).