10X Visium - Mouse Olfactory Bulb

Info

tenx_visium/visium/mouse_olfactory_bulb
10x Genomics (2022)
29.91 MiB
23-09-2024
1184 cells × 13291 genes

Quick links

Source

Used in

• Spatially Variable Genes
  

DATASET ID

tenx_visium/visium/mouse_olfactory_bulb

REFERENCE

10x Genomics (2022)

SIZE

29.91 MiB

CREATED

23-09-2024

DIMENSIONS

1184 × 13291

Description

The tissue was embedded and cryosectioned as described in Visium Spatial Protocols Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides, then fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

Preview

dataset is an AnnData object with n_obs × n_vars = 1184 × 13291 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	13291
feature_name	A human-readable name for the feature, usually a gene symbol.	vector	object	13291
layers
counts	Raw counts	sparsematrix	float32	1184 × 13291
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: 1184 × 13291

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: 13291

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: 13291

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

References

10x Genomics. 2022. “Adult Mouse Olfactory Bulb.” https://www.10xgenomics.com/datasets/adult-mouse-olfactory-bulb-1-standard-1.