10X Visium - Human Skin Melanoma
Gene expression library of Human Skin Melanoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set
Description
10x Genomics obtained FFPE Human Melanoma tissue blocks from Avaden Biosciences. The tissue was sectioned as described in Visium CytAssist Spatial Gene Expression for FFPE Tissue Preparation Guide Demonstrated Protocol (CG000518). Tissue sections of 5 µm was placed on a standard glass slide, deparaffinized followed by immunofluorescence (IF) staining. Sections were coverslipped with 85% glycerol, imaged, decoverslipped, followed by dehydration & decrosslinking Demonstrated Protocol (CG000519). The glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression slide. The probe extension and library construction steps follow the standard Visium for FFPE workflow outside of the instrument.
Preview
An AnnData object with
n_obs × n_vars = 3,455 × 17,874 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 | 17874 |
feature_name | A human-readable name for the feature, usually a gene symbol. | vector | object | 17874 |
| layers | ||||
counts | Raw counts | sparsematrix | float32 | 3455 × 17874 |
| 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_skin_melanoma/dataset.h5ad Used in
References
- 10x Genomics. (2022). Human melanoma, IF stained (FFPE). link ↗