10X Visium - Mouse Brain Coronal

Gene expression library of Mouse Brain (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set

tenx_visium

Info

tenx_visium/visium/mouse_brain_coronal
10x Genomics (2022)
66.22 MiB
23-09-2024
2310 cells × 13985 genes

Used in

Description

FFPE Mouse Brain tissue blocks sectioned as described in Visium CytAssist Spatial Gene Expression for FFPE - Tissue Preparation Guide Demonstrated Protocol. The H&E stained 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. The H&E image was acquired using Olympus VS200 Slide Scanning Microscope. Sequencing depth was 53,497 reads per spot. Sequencing configuration: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 90bp read 2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode. Key metrics include: 2,310 spots detected under tissue; 6,736 median genes per spot; 24,862 median UMI counts per spot.

Preview

dataset is an AnnData object with n_obs × n_vars = 2310 × 13985 with slots:

Reference

Name Description Type Data type Size
var
feature_id Unique identifier for the feature, usually a ENSEMBL gene id. vector object 13985
feature_name A human-readable name for the feature, usually a gene symbol. vector object 13985
layers
counts Raw counts sparsematrix float32 2310 × 13985
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. “Mouse Brain Coronal Section 1 (FFPE).” https://www.10xgenomics.com/datasets/mouse-brain-coronal-section-1-ffpe-2-standard.