10X Visium - Human Skin Melanoma

Gene expression library of Human Skin Melanoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

tenx_visium

Info

tenx_visium/visium/human_skin_melanoma
10x Genomics (2022)
97.92 MiB
23-09-2024
3455 cells × 17874 genes

Used in

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

dataset is an AnnData object with n_obs × n_vars = 3455 × 17874 with slots:

Reference

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

References

10x Genomics. 2022. “Human Melanoma, IF Stained (FFPE).” https://www.10xgenomics.com/datasets/human-melanoma-if-stained-ffpe-2-standard.