Seqfish - Mouse Organogenesis

Info

zenodo_spatial/mouse_organogenesis_seqfish
Lohoff et al. (2021)
15.53 MiB
20-08-2024
19402 × 351

Quick links

Source

Used in

• Spatially variable genes
  

DATASET ID

zenodo_spatial/mouse_organogenesis_seqfish

REFERENCE

Lohoff et al. (2021)

SIZE

15.53 MiB

CREATED

20-08-2024

DIMENSIONS

19402 × 351

Description

Sagittal sections from mouse embryo at the 8-12 ss was profiled by seqFISH.

Preview

dataset is an AnnData object with n_obs × n_vars = 19402 × 351 with slots:

• var: 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
var
feature_name	A human-readable name for the feature, usually a gene symbol.	vector	object	351
layers
counts	Raw counts	sparsematrix	float32	19402 × 351
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: 19402 × 351

Raw counts

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_name']

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

Type: vector, data type: object, shape: 351

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

References

Lohoff, T., S. Ghazanfar, A. Missarova, N. Koulena, N. Pierson, J. A. Griffiths, E. S. Bardot, et al. 2021. “Integration of Spatial and Single-Cell Transcriptomic Data Elucidates Mouse Organogenesis.” Nature Biotechnology 40 (1): 74–85. https://doi.org/10.1038/s41587-021-01006-2.