Seqfish - Mouse Organogenesis

Single-cell spatial expression of mouse organogenesis.

reference Lohoff et al., 2021

Mus musculus Organism

19,402 × 351 Dimensions

15.53 MiB Size

log_cp10k Normalization

26-09-2024 Created

Source

Description

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

Preview

An AnnData object with n_obs × n_vars = 19,402 × 351 with slots:

var: 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
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

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 15.53 MiB

Download

s3://openproblems-data/resources/datasets/zenodo_spatial/seqfish/mouse_organogenesis_seqfish/dataset.h5ad

Used in

Spatially Variable Genes

References

Lohoff, T., Ghazanfar, S., Missarova, A., Koulena, N., Pierson, N., Griffiths, J. A., Bardot, E. S., Eng, C.-H. L., Tyser, R. C. V., Argelaguet, R., Guibentif, C., Srinivas, S., Briscoe, J., Simons, B. D., Hadjantonakis, A.-K., Göttgens, B., Reik, W., Nichols, J., Cai, L., & Marioni, J. C. (2021). Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. 10.1038/s41587-021-01006-2 ↗