Stereo-seq - Drosophila embryo E7
Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.
Description
Drosophila has long been a successful model organism in multiple biomedical fields. Spatial gene expression patterns are critical for the understanding of complex pathways and interactions, whereas temporal gene expression changes are vital for studying highly dynamic physiological activities. Systematic studies in Drosophila are still impeded by the lack of spatiotemporal transcriptomic information. Here, utilizing spatial enhanced resolution omics-sequencing (Stereo-seq), we dissected the spatiotemporal transcriptomic changes of developing Drosophila with high resolution and sensitivity. (Data from an embryo collected 14-16 h after egg laying)
Preview
An AnnData object with
n_obs × n_vars = 1,039 × 755 with slots:
Data structure
| Name | Description | Type | Data type | Size |
|---|---|---|---|---|
| var | ||||
feature_name | A human-readable name for the feature, usually a gene symbol. | vector | object | 755 |
| layers | ||||
counts | Raw counts | sparsematrix | int64 | 1039 × 755 |
| 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.
s3://openproblems-data/resources/datasets/zenodo_spatial/stereoseq/drosophila_embryo_e7/dataset.h5ad Used in
References
- Wang, M., Hu, Q., Lv, T., Wang, Y., Lan, Q., Xiang, R., Tu, Z., Wei, Y., Han, K., Shi, C., Guo, J., Liu, C., Yang, T., Du, W., An, Y., Cheng, M., Xu, J., Lu, H., Li, W., … Liu, L. (2022). High-resolution 3D spatiotemporal transcriptomic maps of developing drosophila embryos and larvae. 10.1016/j.devcel.2022.04.006 ↗