10X Visium - Human Breast Cancer 1

Info

10x_datasets/human_breast_cancer_1_visium
10x Genomics (2020)
75.54 MiB
20-08-2024
4261 × 14906

Quick links

Source

Used in

• Spatially variable genes
  

DATASET ID

10x_datasets/human_breast_cancer_1_visium

REFERENCE

10x Genomics (2020)

SIZE

75.54 MiB

CREATED

20-08-2024

DIMENSIONS

4261 × 14906

Description

10X Genomics obtained fresh frozen human Invasive Lobular Carcinoma breast tissue from BioIVT Asterand. 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 and 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 = 4261 × 14906 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	14906
feature_name	A human-readable name for the feature, usually a gene symbol.	vector	object	14906
layers
counts	Raw counts	sparsematrix	float32	4261 × 14906
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: 4261 × 14906

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: 14906

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: 14906

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

References

10x Genomics. 2020. “Human Breast Cancer: Whole Transcriptome Analysis.” https://www.10xgenomics.com/datasets/human-breast-cancer-whole-transcriptome-analysis-1-standard-1-2-0.