10X Visium - Human Breast Cancer 2
Gene expression library of Human Breast Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set
Description
10x Genomics obtained FFPE human breast tissue from BioIVT Asterand Human Tissue Specimens. The tissue was annotated with Ductal Carcinoma In Situ, Invasive Carcinoma. The tissue was sectioned as described in Visium Spatial Gene Expression for FFPE - Tissue Preparation Guide Demonstrated Protocol (CG000408). Tissue sections of 5 µm were placed on Visium Gene Expression slides, then stained following Deparaffinization, H&E Staining, Imaging & Decrosslinking Demonstrated Protocol (CG000409).
Preview
An AnnData object with
n_obs × n_vars = 2,518 × 13,311 with slots:
Data structure
| Name | Description | Type | Data type | Size |
|---|---|---|---|---|
| var | ||||
feature_id | Unique identifier for the feature, usually a ENSEMBL gene id. | vector | object | 13311 |
feature_name | A human-readable name for the feature, usually a gene symbol. | vector | object | 13311 |
| layers | ||||
counts | Raw counts | sparsematrix | float32 | 2518 × 13311 |
| 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 |
Download & explore
The processed dataset lives on the OpenProblems public S3 bucket, which is world-readable. Download the file directly, or copy its S3 URI to fetch it with your tool of choice.
s3://openproblems-data/resources/datasets/tenx_visium/visium/human_breast_cancer_2/dataset.h5ad Used in
References
- 10x Genomics. (2021). Human breast cancer: Ductal carcinoma in situ, invasive carcinoma (FFPE). link ↗