Details
| Technique | Slide-seq |
|---|---|
| Title | Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution |
| PMID | 30923225 |
| Description | Slide-seq, a method for transferring RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. Using Slide-seq, they localized cell types identified by single-cell RNA sequencing datasets within the cerebellum and hippocampus, characterized spatial gene expression patterns in the Purkinje layer of mouse cerebellum, and defined the temporal evolution of cell type-specific responses in a mouse model of traumatic brain injury. |
| Source | a coronal section of mouse hippocampus, 66 sagittal tissue sections from a single dorsal mouse hippocampus |
| Species | mouse |
| No. genes | >20000 genes |
| No. cells | NA |
| Resolution | 10 um |
| Data normalization | custom normalization method |
| Data availability | Raw image data of pucks, raw sequencing data, processed Slide-seq data, and NMFreg dependencies are available at the Broad institute’s single-cell repository (https://portals.broadinstitute.org/single_cell/study/slide-seq-study). |
Spatially variable (SV) genes
SV genes identified by SpatialDE (Q-value<0.05)
| ID | Gene | Species | Tissue | Puck | P-value | Q-value |
|---|---|---|---|---|---|---|
| ID | Gene | Species | Tissue | Puck | P-value | Q-value |
Functional enrichment analysis of SV genes
GO enrichment analysis of SV genes identified by SpatialDE (Q-value<0.05) in mouese liver.
KEGG enrichment analysis of SV genes identified by SpatialDE (Q-value<0.05) in mouse liver.
GO enrichment analysis of SV genes identified by SpatialDE (Q-value<0.05) in mouse sagittal cerebellum.
KEGG enrichment analysis of SV genes identified by SpatialDE (Q-value<0.05) in mouse sagittal cerebellum.
GO enrichment analysis of SV genes identified by SpatialDE (Q-value<0.05) in mouse sagittal cortex.
KEGG enrichment analysis of SV genes identified by SpatialDE (Q-value<0.05) in mouse sagittal cortex.
GO enrichment analysis of SV genes identified by SpatialDE (Q-value<0.05) in mouse coronal hippocampus.
KEGG enrichment analysis of SV genes identified by SpatialDE (Q-value<0.05) in mouse coronal hippocampus.
