10X Post Xenium - Human Colon

Gene expression library of Post Xenium Human Colon Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set - Replicate 1

reference 10x Genomics, 2023

Homo sapiens Organism

5,561 × 14,016 Dimensions

82.81 MiB Size

log_cp10k Normalization

26-09-2024 Created

Source

Description

This dataset is provided as part of the Technical Note: Post-Xenium In Situ Applications: Immunofluorescence, H&E, and Visium CytAssist Spatial Gene Expression (CG000709). Post-Xenium samples were compared to controls (samples not processed through the Xenium workflow) using 5 µm (FFPE) serial sections.

Preview

An AnnData object with n_obs × n_vars = 5,561 × 14,016 with slots:

var: feature_id , feature_name

layers: counts

uns: dataset_description , dataset_id , dataset_name , dataset_organism , dataset_reference , dataset_summary , dataset_url

Data structure

Name	Description	Type	Data type	Size
var
`feature_id`	Unique identifier for the feature, usually a ENSEMBL gene id.	vector	object	14016
`feature_name`	A human-readable name for the feature, usually a gene symbol.	vector	object	14016
layers
`counts`	Raw counts	sparsematrix	float32	5561 × 14016
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 82.81 MiB

Download

s3://openproblems-data/resources/datasets/tenx_visium/post_xenium/human_colon_cancer/dataset.h5ad

Used in

Spatially Variable Genes

References

10x Genomics. (2023). Visium CytAssist gene expression libraries of post-xenium human colon cancer (FFPE). link ↗