Slide-tags - Mouse Embryo

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.

reference Russell et al., 2023

Mus musculus Organism

4,623 × 14,649 Dimensions

70.21 MiB Size

log_cp10k Normalization

26-09-2024 Created

Source

Description

Mouse embryo tonsil was profiled by Slide-tags.

Preview

An AnnData object with n_obs × n_vars = 4,623 × 14,649 with slots:

obs: cell_type

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
obs
`cell_type`	Classification of the cell type based on its characteristics and function within the tissue or organism.	vector	category	4623
var
`feature_id`	Unique identifier for the feature, usually a ENSEMBL gene id.	vector	object	14649
`feature_name`	A human-readable name for the feature, usually a gene symbol.	vector	object	14649
layers
`counts`	Raw counts	sparsematrix	float32	4623 × 14649
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 70.21 MiB

Download

s3://openproblems-data/resources/datasets/zenodo_spatial_slidetags/slidetags/mouse_embryo/dataset.h5ad

Used in

Spatially Variable Genes

References

Russell, A. J. C., Weir, J. A., Nadaf, N. M., Shabet, M., Kumar, V., Kambhampati, S., Raichur, R., Marrero, G. J., Liu, S., Balderrama, K. S., Vanderburg, C. R., Shanmugam, V., Tian, L., Iorgulescu, J. B., Yoon, C. H., Wu, C. J., Macosko, E. Z., & Chen, F. (2023). Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. 10.1038/s41586-023-06837-4 ↗