DBiT-seq - Mouse Whole Body 1 (E11)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

reference Liu et al., 2020

Mus musculus Organism

1,840 × 7,068 Dimensions

8.29 MiB Size

log_cp10k Normalization

26-09-2024 Created

Source

Description

Gene expression library of an E11 whole mouse embryo tissue profiled using DBiT-seq.

Preview

An AnnData object with n_obs × n_vars = 1,840 × 7,068 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	7068
layers
`counts`	Raw counts	densematrix	float32	1840 × 7068
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 8.29 MiB

Download

s3://openproblems-data/resources/datasets/zenodo_spatial/dbitseq/mouse_e11_1/dataset.h5ad

Used in

Spatially Variable Genes

References

Liu, Y., Yang, M., Deng, Y., Su, G., Enninful, A., Guo, C. C., Tebaldi, T., Zhang, D., Kim, D., Bai, Z., Norris, E., Pan, A., Li, J., Xiao, Y., Halene, S., & Fan, R. (2020). High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. 10.1016/j.cell.2020.10.026 ↗