a database for spatially resolved transcriptomes

Dataset 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).

Browse spatial gene expression

ENSEMBL ID:     Please input ENSEMBL ID: such as ENSMUSG00000092341, ENSMUSG00000019943.
Gene:     Please input gene symbol: such as Malat1, Atp2b1.
Tissue:     Please select tissue to browse.
Puck:     Please select puck for each tissue.
Log:     Please select log transformation of data.
Size:     Please input the size of symbol.
Symbol:     Please select a symbol to display.

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