10X Visium - Human Heart MI 1

Gene expression library of human heart using 10x Visium

zenodo_spatial

Info

zenodo_spatial/visium/human_heart_myocardial_infarction_1
Kuppe et al. (2022)
45.2 MiB
23-09-2024
4269 × 13236

Used in

Description

Frozen heart samples were embedded in OCT (Tissue-Tek) and cryosectioned (Thermo Cryostar). The 10-µm section was placed on the pre-chilled Optimization slides (Visium, 10X Genomics, PN-1000193) and the optimal lysis time was determined. The tissues were treated as recommended by 10X Genomics and the optimization procedure showed an optimal permeabilization time of 12 or 18 min of digestion and release of RNA from the tissue slide. Spatial gene expression slides (Visium, 10X Genomics, PN-1000187) were used for spatial transcriptomics following the Visium User Guides

Preview

dataset is an AnnData object with n_obs × n_vars = 4269 × 13236 with slots:

Reference

Name Description Type Data type Size
var
feature_id Unique identifier for the feature, usually a ENSEMBL gene id. vector object 13236
feature_name A human-readable name for the feature, usually a gene symbol. vector object 13236
layers
counts Raw counts sparsematrix float32 4269 × 13236
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

Kuppe, Christoph, Ricardo O Ramirez Flores, Zhijian Li, Sikander Hayat, Rebecca T Levinson, Xian Liao, Monica T Hannani, et al. 2022. “Spatial Multi-Omic Map of Human Myocardial Infarction.” Nature 608 (7924): 766–77.