10X Visium - Mouse Embryo

Gene expression library of Mouse Embryo (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set

tenx_visium

Info

tenx_visium/visium/mouse_embryo
10x Genomics (2023)
246.08 MiB
23-09-2024
6434 cells × 19288 genes

Used in

Description

The tissue was sectioned as described in Visium CytAssist Spatial Gene Expression for FFPE Tissue Preparation Guide Demonstrated Protocol CG000518. Tissue sections of 5 µm was placed on a standard glass slide, and H&E-stained following deparaffinization. Sections were coverslipped with 85% glycerol, imaged, decoverslipped, followed by dehydration & decrosslinking (Demonstrated Protocol CG000520). The glass slide with the tissue section was processed with the Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression slide (11 mm Capture Area). The probe extension and library construction steps follow the standard Visium for FFPE workflow outside of the instrument.

Preview

dataset is an AnnData object with n_obs × n_vars = 6434 × 19288 with slots:

Reference

Name Description Type Data type Size
var
feature_id Unique identifier for the feature, usually a ENSEMBL gene id. vector object 19288
feature_name A human-readable name for the feature, usually a gene symbol. vector object 19288
layers
counts Raw counts sparsematrix float32 6434 × 19288
uns
dataset_description Long description of the dataset. atomic str 1
dataset_id A unique identifier for the dataset. This is different from the obs.dataset_id field, which is the identifier for the dataset from which the cell data is derived. atomic str 1
dataset_name A human-readable name for the dataset. atomic str 1
dataset_organism The organism of the sample in the dataset. atomic str 1
dataset_reference Bibtex reference of the paper in which the dataset was published. atomic str 1
dataset_summary Short description of the dataset. atomic str 1
dataset_url Link to the original source of the dataset. atomic str 1

References

10x Genomics. 2023. “Visium CytAssist, Mouse Embryo, 11 Mm Capture Area (FFPE).” https://www.10xgenomics.com/datasets/visium-cytassist-mouse-embryo-11-mm-capture-area-ffpe-2-standard.