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Datasets:
helical-ai
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yolksac_human

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10K<n<100K
Tags:
biology
rna
gene expression
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- ---
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- tags:
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- - biology
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- - rna
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- - gene expression
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- pretty_name: YolkSac Human
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- size_categories:
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- - 10K<n<100K
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- license: cc0-1.0
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- ---
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- **Source:** Human fetal yolk sac scRNA-seq data (sample ID: F158 for Haniffa Lab; 16099 for HDBR)
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-
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- Investigating the blood, immune and stromal cells present in a human fetal embryo in a world first single cell transcriptomic atlas.
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-
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- **Raw File:** [Array Express](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11673) (E-MTAB-11673, [17_04_24_YolkSacRaw_F158_WE_annots.h5ad](https://www.ebi.ac.uk/biostudies/files/E-MTAB-11673/17_04_24_YolkSacRaw_F158_WE_annots.h5ad))
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-
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- **Assay:** 10X 5' transcription profiling
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-
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- **Number of Cells:** 31,680
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-
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- **Number of Genes:** 37,318
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-
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- **Raw counts:** in adata.X
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-
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- There are three levels of cell annotation you can access in the data:
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-
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- | LVL1 | Cell Count |
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- |------------|------------|
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- | ERYTHROID | 9374 |
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- | LYMPHOID | 72 |
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- | MK | 205 |
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- | MYELOID | 7067 |
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- | PROGENITOR | 195 |
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- | STROMA | 14767 |
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-
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-
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- | LVL2 | Cell Count |
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- |-----------------------|------------|
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- | B_CELL | 8 |
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- | CMP | 1 |
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- | DC | 19 |
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- | ELP | 54 |
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- | ENDODERM | 3238 |
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- | ENDOTHELIUM | 1614 |
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- | EOSINOPHIL_BASOPHIL | 3 |
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- | ERYTHROID | 9374 |
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- | FIBROBLAST | 7504 |
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- | HSPC | 71 |
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- | ILC | 32 |
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- | LMPP | 9 |
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- | MACROPHAGE | 6934 |
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- | MAST_CELL | 60 |
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- | MEMP | 50 |
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- | MESOTHELIUM | 1371 |
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- | MK | 205 |
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- | MONO MAC DC2 | 16 |
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- | MONO MAC PRE DC2 | 12 |
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- | MONOCYTE | 1 |
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- | MONOCYTE_MACROPHAGE | 6 |
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- | MONOCYTE_YS_1 | 11 |
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- | MOP | 10 |
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- | NEUTROPHIL_PRECURSOR | 2 |
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- | NK | 16 |
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- | PDC PRECURSOR | 16 |
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- | PROMONOCYTE | 3 |
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- | SMOOTH_MUSCLE | 1040 |
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-
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- | LVL3 | Cell Count |
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- |--------------------------------|------------|
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- | CMP | 1 |
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- | DC2_CYCLING | 2 |
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- | DEF_HSPC_1 | 9 |
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- | DEF_HSPC_2 | 34 |
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- | EARLY_ERYTHROID | 9 |
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- | ELP | 54 |
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- | ENDODERM | 3238 |
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- | ENDOTHELIUM_AEC | 396 |
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- | ENDOTHELIUM_PROLIF_AEC | 77 |
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- | ENDOTHELIUM_PROLIF_SINUSOIDAL_EC | 168 |
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- | ENDOTHELIUM_SINUSOIDAL | 173 |
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- | ENDOTHELIUM_VWF | 246 |
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- | EO_BASO_MAST_PRECURSOR | 3 |
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- | ERYTHROID | 9325 |
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- | FIBROBLAST | 7504 |
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- | HE | 167 |
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- | HSPC_1 | 2 |
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- | HSPC_2 | 3 |
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- | ILC_PRECURSOR | 32 |
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- | IMMATURE_ENDOTHELIUM | 387 |
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- | LMPP | 9 |
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- | LYMPHOID B LIN | 8 |
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- | MAC DC2 | 4 |
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- | MACROPHAGE_IRON_RECYCLING | 3980 |
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- | MACROPHAGE_KUPFFER_LIKE | 1070 |
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- | MACROPHAGE_LYVE1_HIGH | 1327 |
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- | MACROPHAGE_MICROGLIA | 1 |
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- | MACROPHAGE_PRE_MAC | 2 |
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- | MACROPHAGE_PROLIFERATING | 554 |
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- | MAST_CELL | 60 |
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- | MEMP | 50 |
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- | MESOTHELIUM | 1371 |
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- | MID_ERYTHROID | 40 |
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- | MK | 205 |
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- | MONO MAC DC2 | 16 |
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- | MONO MAC PRE DC2 | 12 |
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- | MONOCYTE_0 | 1 |
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- | MONOCYTE_1 | 11 |
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- | MONOCYTE_MACROPHAGE | 6 |
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- | MOP | 10 |
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- | NEUTROPHIL_PRECURSOR | 2 |
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- | NK | 16 |
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- | PDC PRECURSOR | 16 |
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- | PRE DC2 | 13 |
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- | PRIM_HSPC_1 | 20 |
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- | PRIM_HSPC_2 | 3 |
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- | PROMONOCYTE | 3 |
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- | SMOOTH_MUSCLE | 1040 |
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-
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-
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- **License information:** Data was published in EMBL-EBI (Array Express), CC0.
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-
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- These data was used in [Goh et al, Science, 2023](https://www.science.org/doi/10.1126/science.add7564) and the article is licensed under a [BY 4.0](https://creativecommons.org/licenses/by/4.0/) International license.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
dataset_card ADDED
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+ ---
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+ tags:
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+ - biology
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+ - rna
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+ - gene expression
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+ pretty_name: YolkSac Human
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+ size_categories:
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+ - 10K<n<100K
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+ license: cc0-1.0
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+ ---
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+
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+ ## Human fetal yolk sac scRNA-seq data
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+
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+ The yolk sac (YS) generates the first blood and immune cells and provides nutritional and metabolic support to the developing embryo. Our current understanding of its functions derives from pivotal studies in model systems, and insights from human studies are limited. Single-cell genomics technologies have facilitated the interrogation of human developmental tissues at unprecedented resolution. Atlases of blood and immune cells from multiple organs have been greatly enhanced by focused, time-resolved analyses of specific tissues.
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+
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+ ### Project information
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+
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+ - **Source:** Human fetal yolk sac scRNA-seq data
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+ - Female donor, Carnegie Stage 17
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+ - **Sample ID:**
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+ - F158 for Haniffa Lab
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+ - 16099 for HDBR
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+ - **Raw file:**
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+ - [Array Express (E-MTAB-11673)](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11673)
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+ - [17_04_24_YolkSacRaw_F158_WE_annots.h5ad](https://www.ebi.ac.uk/biostudies/files/E-MTAB-11673/17_04_24_YolkSacRaw_F158_WE_annots.h5ad)
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+
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+ ### Assay details
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+
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+ - **Assay:** 10X 5' transcription profiling
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+ - **Number of Cells:** 31,680
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+ - **Number of Genes:** 37,318
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+
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+ ### Load the data
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+
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+ Load the dataset using Huggingface's optimized library and create the AnnData object:
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+
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+ ```
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+ from datasets import load_dataset
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+ ds = load_dataset("helical-ai/yolksac_human",trust_remote_code=True, split="train[:65%]",download_mode="reuse_cache_if_exists")
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+ ds = ds.with_format("np")
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+ ```
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+
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+ ```
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+ observation_columns = [obs for obs in list(ds.features.keys()) if not obs == 'raw_counts']
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+ obs_data = pd.DataFrame(ds.select_columns(observation_columns).data.to_pandas(),columns=observation_columns)
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+ adata = ad.AnnData(ds['raw_counts'],obs=obs_data)
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+ adata.var_names = ds.features['raw_counts'].id.split(",")
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+ adata.var['gene_name'] = adata.var_names.str.upper()
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+ ```
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+
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+ ### Cell type annotation
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+
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+ There are three levels of cell annotation you can access in the data:
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+
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+ | Annotation Granularity Level | Cell Type Names |
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+ |------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------|
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+ | `Level 1 (LVL1)` | ERYTHROID, LYMPHOID, MK, MYELOID, PROGENITOR, STROMA |
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+ | `Level 2 (LVL2)` | B_CELL, CMP, DC, ELP, ENDODERM, ENDOTHELIUM, EOSINOPHIL_BASOPHIL, ERYTHROID, FIBROBLAST, HSPC, ILC, LMPP, MACROPHAGE, MAST_CELL, MEMP, MESOTHELIUM, MK, MONO MAC DC2, MONO MAC PRE DC2, MONOCYTE, MONOCYTE_MACROPHAGE, MONOCYTE_YS_1, MOP, NEUTROPHIL_PRECURSOR, NK, PDC PRECURSOR, PROMONOCYTE, SMOOTH_MUSCLE |
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+ | `Level 3 (LVL3)` | CMP, DC2_CYCLING, DEF_HSPC_1, DEF_HSPC_2, EARLY_ERYTHROID, ELP, ENDODERM, ENDOTHELIUM_AEC, ENDOTHELIUM_PROLIF_AEC, ENDOTHELIUM_PROLIF_SINUSOIDAL_EC, ENDOTHELIUM_SINUSOIDAL, ENDOTHELIUM_VWF, EO_BASO_MAST_PRECURSOR, ERYTHROID, FIBROBLAST, HE, HSPC_1, HSPC_2, ILC_PRECURSOR, IMMATURE_ENDOTHELIUM, LMPP, LYMPHOID B LIN, MAC DC2, MACROPHAGE_IRON_RECYCLING, MACROPHAGE_KUPFFER_LIKE, MACROPHAGE_LYVE1_HIGH, MACROPHAGE_MICROGLIA, MACROPHAGE_PRE_MAC, MACROPHAGE_PROLIFERATING, MAST_CELL, MEMP, MESOTHELIUM, MID_ERYTHROID, MK, MONO MAC DC2, MONO MAC PRE DC2, MONOCYTE_0, MONOCYTE_1, MONOCYTE_MACROPHAGE, MOP, NEUTROPHIL_PRECURSOR, NK, PDC PRECURSOR, PRE DC2, PRIM_HSPC_1, PRIM_HSPC_2, PROMONOCYTE, SMOOTH_MUSCLE |
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+
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+
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+ ### License information
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+
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+ Data was published in EMBL-EBI (Array Express), CC0.
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+
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+ These data was used in [Goh et al, Science, 2023](https://www.science.org/doi/10.1126/science.add7564) and the article is licensed under a [BY 4.0](https://creativecommons.org/licenses/by/4.0/) International license.