ssread - ssREAD

Summary

Publication

Title: Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Authors: Kristen R. Maynard, Leonardo Collado-Torres, Lukas M. Weber, Cedric Uytingco, Brianna K. Barry, Stephen R. Williams, Joseph L. Catallini II, Matthew N. Tran, Zachary Besich, Madhavi Tippani, Jennifer Chew, Yifeng Yin, Joel E. Kleinman, Thomas M. Hyde, Nikhil Rao, Stephanie C. Hicks, Keri Martinowich & Andrew E. Jaffe$

Date published: 2/21/21

Date added: 5/1/22

Journal: Nature Neuroscience

DOI: 10.1038/s41593-020-00787-0

Protocol: 10x Genomics Visium

Data source: https://github.com/LieberInstitute/HumanPilot

Study design

Species: human

Number of samples: 12

Region: Dorsolateral prefrontal cortex

Experimental factors:

Disease
Brain disorder
Age
Sex
Inferred cell type - authors labels

Figure: Spatial transcriptomics in DLPFC using Visium.

Spot-level data

Current selection:

ssREAD sample ID:

Total spots in the plot: 4226

Clusters to plot:

Toggle raw image: false

Point size:

Image opacity:

0.4

Point opacity:

Gene expression

Please enter a gene symbol.

Spatially variable genes

Sample:

Log2 fold-change cutoff:

0.5

Adjusted p-value cutoff:

10^-6

10^-5

10^-4

10^-3

0.01

0.05

0.1

Foldchange direction:

All

Down

Sort by
NRGN	1.86124	0.00e+0	0.863	0.157	0.055	1.726	0.785
SLC17A7	1.57429	0.00e+0	0.736	0.103	0.036	1.472	0.515
CHN1	1.39231	0.00e+0	0.899	0.321	0.112	1.798	1.605
RORB	1.34588	0.00e+0	0.360	0.032	0.011	0.72	0.160
TMSB10	1.21375	0.00e+0	0.712	0.198	0.069	1.424	0.990
CAMK2A	1.19418	0.00e+0	0.807	0.257	0.090	1.614	1.285
NECAB1	1.15875	0.00e+0	0.562	0.092	0.032	1.124	0.460
PRKCB	1.12511	0.00e+0	0.738	0.207	0.072	1.476	1.035
ENC1	1.1232	0.00e+0	0.625	0.151	0.053	1.25	0.755
PTK2B	1.10001	0.00e+0	0.460	0.070	0.025	0.92	0.350
NEUROD2	1.09732	0.00e+0	0.366	0.028	0.010	0.732	0.140
LMO4	1.06687	0.00e+0	0.538	0.097	0.034	1.076	0.485
TBR1	1.05181	0.00e+0	0.345	0.023	0.008	0.69	0.115
PHYHIP	1.02681	0.00e+0	0.768	0.289	0.101	1.536	1.445
SV2B	1.02608	0.00e+0	0.380	0.035	0.012	0.76	0.175

Differential expression (DE) / Gene set enrichment

Sample:

Note: The MAST package were used to calculate DEGs on normalized gene expression data (parameter: log2FC > 0.25, adj.p-value < 0.05).

Group:

Cluster:

Log2 fold-change cutoff:

0.5

Adjusted p-value cutoff:

10^-6

10^-5

10^-4

10^-3

0.01

0.05

0.1

DE direction:

All

Down

Sort by
GPR98	2.2986	0.916	0.134	0.00e+0

Deconvolution

Spatial sample:

scRNA-seq dataset:

Showing results: ST00109 and AD00101