theislab / neural_organoid_atlas

Reproducibility repository for the Human Neural Organoid Atlas publication

The Human Neural Organoid Atlas (HNOCA)

Reproducibility repository for the Human Neural Organoid Atlas preprint.

He, Z.; Dony, L.; Fleck, J. S. et al. An integrated transcriptomic cell atlas of human neural organoids. bioRxiv 2023.10.05.561097; doi: 10.1101/2023.10.05.561097

Code availability

Note 🚧 We are currently collecting and uploading all notebooks used in this analysis. This note wil disappear as soon as all code has been made available via this page.

Directory structure:

• figures/ contains scripts to reproduce the plots from the figures in the manuscript.
• notebooks/ contains the code used to construct, preprocess and annotate HNOCA, compute the transcriptomic similarity comparison and differential compositional analysis.
• integration_evaluation/ contains the script for scVI, scPoli, and scANVI integration of HNOCA which were used in the integration benchmarking as well as the script to compute the benchmarking.
• primary_mapping/ contains scripts to train a scANVI model on the HDBCA data and map organoid data onto it.
• NOMS_mapping/ contains scripts for mapping the neural organoid morphogen screen (NOMS) data onto the HNCOA and primary HDBCA data.
• protocol_composition/ contains scripts to perform compositional analysis between organoid protocols.
• pseudotime/ contains scripts to compute a real time-informed pseudotime with moscot neural OT.
• supplemental_files/ contains:
  • Snapseed input file containing our celltype hierarchy with associated marker genes
  • Model parameters of our scPoli integration model
  • scPoli sample embedding of HNOCA

Data availability

An pre-release version comprised of the public portion of HNOCA is avalable for download here. Download details: hnoca_pre-release_public_subset.h5ad (40.5 GB).

HNOCA pre-release metadata legend

.obs keys legend

* sfaira-controlled metadata, most controlled by the respective ontology. see here for more details: https://sfaira.readthedocs.io/en/latest/adding_datasets.html#dataset-or-observation-wise

** original values provided in the datasets prior to ontology matching (only available for ontology-controlled sfaira metadata fields)

.obs key	Description
annot_level_1	Level 1 of the final cell-type annotation hierarchy
annot_level_2	Level 2 of the final cell-type annotation hierarchy
annot_level_3	Level 3 of the final cell-type annotation hierarchy
annot_level_4	Level 4 of the final cell-type annotation hierarchy
annot_region	Final brain region annotation for neuronal cells
assay_sc	*
assay_differentiation	*
assay_type_differentiation	*
bio_sample	*
cell_line	*
cell_type	*
development_stage	*
disease	*
ethnicity	*
gm	*
individual	*
organ	*
organism	*
sex	*
state_exact	*
sample_source	*
source_doi	*
tech_sample	*
treatment	*
assay_sc_original	**
cell_line_original	**
cell_type_original	**
development_stage_original	**
disease_original	**
ethnicity_original	**
organ_original	**
organism_original	**
sex_original	**
id	Unique sfaira sample ID
suspension_type	Single nuclei or single cells
suspension_type_original	Single nuclei or single cells
obs_names_original	Original obs annotation in the author-provided dataset
organoid_age_days	Organoid age in dayys at the time of experiment
publication	First Author, Year for the source publication of the dataset
doi	DOI for the source publication of the dataset
batch	Concatenation of the columns id, bio_sample and tech_sample
n_genes_by_counts	Number of genes with >0 counts
log1p_n_genes_by_counts	natural logarithm of number of genes with >0 counts +1
total_counts	total UMI count of this cell
log1p_total_counts	Natural logarithm of the total UMI count of this cell +1
total_counts_mt	Total mitochondrial UMI count
log1p_total_counts_mt	Natural logarithm of total mitochondrial UMI count +1
pct_counts_mt	Percentage of UMI counts mapped to mitochindrial genes
leiden_pca_unintegrated_1	Leiden clustering (resolution=1) of unintegrated PCA-derived knn graph
leiden_pca_unintegrated_80	Leiden clustering (resolution=80) of unintegrated PCA-derived knn graph
leiden_pca_rss_1	Leiden clustering (resolution=1) of pre-integrated RSS-PCA-derived knn graph
leiden_pca_rss_80	Leiden clustering (resolution=80) of pre-integrated RSS-PCA-derived knn graph
leiden_scpoli_1	Leiden clustering (resolution=1) of integrated scPoli embedding-derived knn graph
leiden_scpoli_80	Leiden clustering (resolution=80) of integrated scPoli embedding-derived knn graph
snapseed_pca_unintegrated_level_1	Level 1 label of automatic cell type annotation (snapseed) from unintegrated PCA representation
snapseed_pca_unintegrated_level_2	Level 2 label of automatic cell type annotation (snapseed) from unintegrated PCA representation
snapseed_pca_unintegrated_level_3	Level 3 label of automatic cell type annotation (snapseed) from unintegrated PCA representation
snapseed_pca_unintegrated_level_4	Level 4 label of automatic cell type annotation (snapseed) from unintegrated PCA representation
snapseed_pca_unintegrated_level_5	Level 5 label of automatic cell type annotation (snapseed) from unintegrated PCA representation
snapseed_pca_unintegrated_level_12	Merged level 1,2 annotations from unintegrated PCA representation (iterative replacement of NAs with higher-level labels)
snapseed_pca_unintegrated_level_123	Merged level 1,2,3 annotations from unintegrated PCA representation (iterative replacement of NAs with higher-level labels)
snapseed_pca_unintegrated_level_1234	Merged level 1,2,3,4 annotations from unintegrated PCA representation (iterative replacement of NAs with higher-level labels)
snapseed_pca_unintegrated_level_12345	Merged level 1,2,3,4,5 annotations from unintegrated PCA representation (iterative replacement of NAs with higher-level labels)
snapseed_pca_rss_level_1	Level 1 label of automatic cell type annotation (snapseed) from pre-integrated RSS-PCA representation
snapseed_pca_rss_level_2	Level 2 label of automatic cell type annotation (snapseed) from pre-integrated RSS-PCA representation
snapseed_pca_rss_level_3	Level 3 label of automatic cell type annotation (snapseed) from pre-integrated RSS-PCA representation
snapseed_pca_rss_level_4	Level 4 label of automatic cell type annotation (snapseed) from pre-integrated RSS-PCA representation
snapseed_pca_rss_level_5	Level 5 label of automatic cell type annotation (snapseed) from pre-integrated RSS-PCA representation
snapseed_pca_rss_level_12	Merged level 1,2 annotations from pre-integrated RSS-PCA representation (iterative replacement of NAs with higher-level labels)
snapseed_pca_rss_level_123	Merged level 1,2,3 annotations from pre-integrated RSS-PCA representation (iterative replacement of NAs with higher-level labels)
snapseed_pca_rss_level_1234	Merged level 1,2,3,4 annotations from pre-integrated RSS-PCA representation (iterative replacement of NAs with higher-level labels)
snapseed_pca_rss_level_12345	Merged level 1,2,3,4,5 annotations from pre-integrated RSS-PCA representation (iterative replacement of NAs with higher-level labels)
snapseed_scpoli_level_1	Level 1 label of automatic cell type annotation (snapseed) from integrated scPoli representation
snapseed_scpoli_level_2	Level 2 label of automatic cell type annotation (snapseed) from integrated scPoli representation
snapseed_scpoli_level_3	Level 3 label of automatic cell type annotation (snapseed) from integrated scPoli representation
snapseed_scpoli_level_4	Level 4 label of automatic cell type annotation (snapseed) from integrated scPoli representation
snapseed_scpoli_level_5	Level 5 label of automatic cell type annotation (snapseed) from integrated scPoli representation
snapseed_scpoli_level_12	Merged level 1,2 annotations from integrated scPoli representation (iterative replacement of NAs with higher-level labels)
snapseed_scpoli_level_123	Merged level 1,2,3 annotations from integrated scPoli representation (iterative replacement of NAs with higher-level labels)
snapseed_scpoli_level_1234	Merged level 1,2,3,4 annotations from integrated scPoli representation (iterative replacement of NAs with higher-level labels)
snapseed_scpoli_level_12345	Merged level 1,2,3,4,5 annotations from integrated scPoli representation (iterative replacement of NAs with higher-level labels)
ECM_raw	Binary morphogen indicator for differentiation protocol: Extra-cellular matrix
ROCK_inhibitor_raw	Binary morphogen indicator for differentiation protocol: ROCK inhibitor
BMP_activator_raw	Binary morphogen indicator for differentiation protocol: BMP activator
TGF_B_activator_raw	Binary morphogen indicator for differentiation protocol: TGFβ activator
TGF_B_inhibitor_raw	Binary morphogen indicator for differentiation protocol: TGFβ inhibitor
BMP_inhibitor_raw	Binary morphogen indicator for differentiation protocol: BMP inhibitor
WNT_activator_raw	Binary morphogen indicator for differentiation protocol: WNT activator
WNT_inhibitor_raw	Binary morphogen indicator for differentiation protocol: WNT inhibitor
EGF_raw	Binary morphogen indicator for differentiation protocol: EGF
FGF2_raw	Binary morphogen indicator for differentiation protocol: FGF2
FGF8_raw	Binary morphogen indicator for differentiation protocol: FGF8
SHH_agonist_raw	Binary morphogen indicator for differentiation protocol: Sonic hedgehog agonist
RA_raw	Binary morphogen indicator for differentiation protocol: Retinoic acid
MEK_ERK_inhibitor_raw	Binary morphogen indicator for differentiation protocol: MEK/ERK inhibitor
Notch_inhibitor_raw	Binary morphogen indicator for differentiation protocol: Notch Inhibitor

🚧 All data will be released here in due course.