license:cc0-1.0 size_categories:100K<n<1M region:us biology rna gene expression mus musculus (mouse)
---
tags:
- biology
- rna
- gene expression
- mus musculus (mouse)
pretty_name: Mouse Gastrulation
size_categories:
- 100K<n<1M
license: cc0-1.0
---
## Mouse Gastrulation scRNA-seq data

Across the animal kingdom, gastrulation represents a key developmental event during which embryonic pluripotent cells diversify into lineage-specific precursors that will generate the adult organism. 

### Project information

- **Source:** scRNA-seq whole mouse embryos during gastrulation and organoienesis, spanning days 6.5 to 8.5 of development, including embryonic and extraembryonic tissues.  

- **Raw file:**
  - [Array Express (E-MTAB-6967)](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6967)
- **Species**
  - Mus musculus (Mouse)

### Assay details

- **Assay:** 10X Genomics Chromium system (version 1 chemistry)
- **Number of Cells:** 139,331
- **Number of Genes:** 29,452

### Load the data
Load the dataset using Huggingface's optimized library and create the AnnData object:

```
from datasets import load_dataset
from scipy.sparse import lil_matrix
ds = load_dataset("helical-ai/gastrulation_mmusculus",trust_remote_code=True, split="train[:65%]",download_mode="reuse_cache_if_exists")
```

```
observation_columns = [obs for obs in list(ds.features.keys()) if not obs == 'raw_counts']
obs_data = pd.DataFrame(ds.select_columns(observation_columns).data.to_pandas(),columns=observation_columns)
lil = lil_matrix((len(ds),ds[0]['size']))
lil.data = np.array(ds['raw_counts'],dtype="object")
lil.rows = np.array(ds['rows'],dtype="object")
ann_data = ad.AnnData(lil.tocsr(),obs=obs_data)
ann_data.var_names = ds.features['raw_counts'].id.split(",")
```

### Key metadata

| Category name              | Types                                                                                      |
|----------------------------|--------------------------------------------------------------------------------------------|
| [1]`stage`                 | E6.5, E6.75, E7.0, E7.25, E7.5, E7.75, E8.0, E8.25, E8.5, mixed_gastrulation                 |
| [2]`sequencing.batch`      | 1, 2, 3                                                                                     |
| [3]`theiler`               | TS10, TS11, TS12, TS9, TS9-10                                                               |
| `celltype`                 | Allantois, Anterior Primitive Streak, Blood progenitors 1, Blood progenitors 2, Cardiomyocytes, Caudal Mesoderm, Caudal epiblast, Caudal neurectoderm, Def. endoderm, Endothelium, Epiblast, Erythroid1, Erythroid2, Erythroid3, ExE ectoderm, ExE endoderm, ExE mesoderm, Forebrain/Midbrain/Hindbrain, Gut, Haematoendothelial progenitors, Intermediate mesoderm, Mesenchyme, Mixed mesoderm, NMP, Nascent mesoderm, Neural crest, Notochord, PGC, Paraxial mesoderm, Parietal endoderm, Pharyngeal mesoderm, Primitive Streak, Rostral neurectoderm, Somitic mesoderm, Spinal cord, Surface ectoderm, Visceral endoderm, nan |

*[1]* Embryonic stages, specific days (E6.5–E8.5), and developmental phases in mouse embryogenesis.  
*[2]* Different sequencing runs, crucial for managing technical variability in experiments.  
*[3]* A staging system used in mouse embryology to describe specific morphological stages of development.

### License information

Data was published in EMBL-EBI (Array Express), CC0. 

This dataset was used in [Pijuan-Sala et al, Nature 2019](https://www.nature.com/articles/s41586-019-0933-9).