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10X Visium - Human Intestine Cancer

Gene expression library of Human Intestinal Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set

reference 10x Genomics, 2022
Homo sapiens Organism
2,660 × 14,292 Dimensions
78.32 MiB Size
log_cp10k Normalization
26-09-2024 Created
Source

Description

5 µm section from Human Intestinal Cancer. FFPE tissue purchased from BioIVT Asterand Human Tissue Specimens. Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A).

Preview

An AnnData object with n_obs × n_vars = 2,660 × 14,292 with slots:

layers: counts

Data structure

Name Description Type Data type Size
var
feature_id Unique identifier for the feature, usually a ENSEMBL gene id. vector object 14292
feature_name A human-readable name for the feature, usually a gene symbol. vector object 14292
layers
counts Raw counts sparsematrix float32 2660 × 14292
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.

dataset.h5ad 78.32 MiB
Download
s3://openproblems-data/resources/datasets/tenx_visium/visium/human_intestinal_cancer/dataset.h5ad

Used in

Spatially Variable Genes

References

  1. 10x Genomics. (2022). Human intestine cancer (FPPE). link ↗