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10X Visium - Human Lymph Node

Whole transcriptome analysis, Human Lymph Node

reference 10x Genomics, 2019
Homo sapiens Organism
4,037 × 15,493 Dimensions
93.98 MiB Size
log_cp10k Normalization
26-09-2024 Created
Source

Description

10x Genomics obtained fresh frozen human lymph node from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide Demonstrated Protocol (CG000240). Tissue sections of 10 µm thickness were placed on Visium Gene Expression Slides.

Preview

An AnnData object with n_obs × n_vars = 4,037 × 15,493 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 15493
feature_name A human-readable name for the feature, usually a gene symbol. vector object 15493
layers
counts Raw counts sparsematrix float32 4037 × 15493
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 93.98 MiB
Download
s3://openproblems-data/resources/datasets/tenx_visium/visium/human_lymph_node/dataset.h5ad

Used in

Spatially Variable Genes

References

  1. 10x Genomics. (2019). Human lymph node. link ↗