Slide-tags - Human Tonsil

Info

zenodo_spatial_slidetags/human_tonsil_slidetags
Russell et al. (2023)
109.49 MiB
20-08-2024
5778 × 17746

Quick links

Source

Used in

• Spatially variable genes
  

DATASET ID

zenodo_spatial_slidetags/human_tonsil_slidetags

REFERENCE

Russell et al. (2023)

SIZE

109.49 MiB

CREATED

20-08-2024

DIMENSIONS

5778 × 17746

Description

A human tonsil was profiled by Slide-tags.

Preview

dataset is an AnnData object with n_obs × n_vars = 5778 × 17746 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

Reference

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	5778
var
feature_id	Unique identifier for the feature, usually a ENSEMBL gene id.	vector	object	17746
feature_name	A human-readable name for the feature, usually a gene symbol.	vector	object	17746
layers
counts	Raw counts	sparsematrix	float32	5778 × 17746
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

Slot crossref data

dataset.layers['counts']

In R: dataset$layers[["counts"]]

Type: sparsematrix, data type: float32, shape: 5778 × 17746

Raw counts

dataset.obs['cell_type']

In R: dataset$obs[["cell_type"]]

Type: vector, data type: category, shape: 5778

Classification of the cell type based on its characteristics and function within the tissue or organism.

dataset.uns['dataset_description']

In R: dataset$uns[["dataset_description"]]

Type: atomic, data type: str, shape: 1

Long description of the dataset.

dataset.uns['dataset_id']

In R: dataset$uns[["dataset_id"]]

Type: atomic, data type: str, shape: 1

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.

dataset.uns['dataset_name']

In R: dataset$uns[["dataset_name"]]

Type: atomic, data type: str, shape: 1

A human-readable name for the dataset.

dataset.uns['dataset_organism']

In R: dataset$uns[["dataset_organism"]]

Type: atomic, data type: str, shape: 1

The organism of the sample in the dataset.

dataset.uns['dataset_reference']

In R: dataset$uns[["dataset_reference"]]

Type: atomic, data type: str, shape: 1

Bibtex reference of the paper in which the dataset was published.

dataset.uns['dataset_summary']

In R: dataset$uns[["dataset_summary"]]

Type: atomic, data type: str, shape: 1

Short description of the dataset.

dataset.uns['dataset_url']

In R: dataset$uns[["dataset_url"]]

Type: atomic, data type: str, shape: 1

Link to the original source of the dataset.

dataset.var['feature_id']

In R: dataset$var[["feature_id"]]

Type: vector, data type: object, shape: 17746

Unique identifier for the feature, usually a ENSEMBL gene id.

dataset.var['feature_name']

In R: dataset$var[["feature_name"]]

Type: vector, data type: object, shape: 17746

A human-readable name for the feature, usually a gene symbol.

References

Russell, Andrew J. C., Jackson A. Weir, Naeem M. Nadaf, Matthew Shabet, Vipin Kumar, Sandeep Kambhampati, Ruth Raichur, et al. 2023. “Slide-Tags Enables Single-Nucleus Barcoding for Multimodal Spatial Genomics.” Nature 625 (7993): 101–9. https://doi.org/10.1038/s41586-023-06837-4.