10X Visium - Human Heart MI 2

Info

zenodo_spatial/visium/human_heart_myocardial_infarction_2
Kuppe et al. (2022)
24.46 MiB
23-09-2024
4518 cells × 10687 genes

Quick links

Source

Used in

• Spatially Variable Genes
  

DATASET ID

zenodo_spatial/visium/human_heart_myocardial_infarction_2

REFERENCE

Kuppe et al. (2022)

SIZE

24.46 MiB

CREATED

23-09-2024

DIMENSIONS

4518 × 10687

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 = 4518 × 10687 with slots:

• var: feature_id, feature_name
  
• layers: counts
  
• uns: dataset_description, dataset_id, dataset_name, dataset_organism, dataset_reference, dataset_summary, dataset_url

Reference

Name	Description	Type	Data type	Size
var
feature_id	Unique identifier for the feature, usually a ENSEMBL gene id.	vector	object	10687
feature_name	A human-readable name for the feature, usually a gene symbol.	vector	object	10687
layers
counts	Raw counts	sparsematrix	float32	4518 × 10687
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

Slot crossref data

dataset.layers['counts']

In R: dataset$layers[["counts"]]

Type: sparsematrix, data type: float32, shape: 4518 × 10687

Raw counts

dataset.uns['dataset_description']

In R: dataset$uns[["dataset_description"]]

Type: atomic, data type: str, shape: 1

Long description of the dataset.

dataset.uns['dataset_id']

In R: dataset$uns[["dataset_id"]]

Type: atomic, data type: str, shape: 1

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.

dataset.uns['dataset_name']

In R: dataset$uns[["dataset_name"]]

Type: atomic, data type: str, shape: 1

A human-readable name for the dataset.

dataset.uns['dataset_organism']

In R: dataset$uns[["dataset_organism"]]

Type: atomic, data type: str, shape: 1

The organism of the sample in the dataset.

dataset.uns['dataset_reference']

In R: dataset$uns[["dataset_reference"]]

Type: atomic, data type: str, shape: 1

Bibtex reference of the paper in which the dataset was published.

dataset.uns['dataset_summary']

In R: dataset$uns[["dataset_summary"]]

Type: atomic, data type: str, shape: 1

Short description of the dataset.

dataset.uns['dataset_url']

In R: dataset$uns[["dataset_url"]]

Type: atomic, data type: str, shape: 1

Link to the original source of the dataset.

dataset.var['feature_id']

In R: dataset$var[["feature_id"]]

Type: vector, data type: object, shape: 10687

Unique identifier for the feature, usually a ENSEMBL gene id.

dataset.var['feature_name']

In R: dataset$var[["feature_name"]]

Type: vector, data type: object, shape: 10687

A human-readable name for the feature, usually a gene symbol.

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.