AnnData object with n_obs × n_vars = 1034819 × 36601 backed at '/gpfs/commons/groups/iossifov_lab/SC_Summaries_GRR/summary/johansen2025Crossspecies/comprehensive_expression_matrix/Human/Human_HMBA_basalganglia_AIT_pre-print.h5ad'
    obs: 'Neighborhood', 'Class', 'Subclass', 'Group', 'Cluster', 'cluster_id', 'cell_type_ontology_term', 'load_id', 'donor_id', 'assay', 'assay_ontology_term_id', 'organism', 'organism_ontology_term_id', 'development_stage', 'anatomical_region', 'anatomical_region_merged', 'anatomical_region_ontology_term_id', 'brain_region_ontology_term_id', 'self_reported_sex', 'self_reported_sex_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'disease', 'disease_ontology_term_id', 'suspension_type', 'is_primary_data', 'atac_confidently_mapped_read_pairs', 'atac_fraction_of_genome_in_peaks', 'atac_fraction_of_high_quality_fragments_in_cells', 'atac_fraction_of_high_quality_fragments_overlapping_tss', 'atac_fraction_of_high_quality_fragments_overlapping_peaks', 'atac_fraction_of_transposition_events_in_peaks_in_cells', 'atac_mean_raw_read_pairs_per_cell', 'atac_median_high_quality_fragments_per_cell', 'atac_non_nuclear_read_pairs', 'atac_number_of_peaks', 'atac_percent_duplicates', 'atac_q30_bases_in_barcode', 'atac_q30_bases_in_read_1', 'atac_q30_bases_in_read_2', 'atac_q30_bases_in_sample_index_i1', 'atac_sequenced_read_pairs', 'atac_tss_enrichment_score', 'atac_unmapped_read_pairs', 'atac_valid_barcodes', 'gex_fraction_of_transcriptomic_reads_in_cells', 'gex_mean_raw_reads_per_cell', 'gex_median_umi_counts_per_cell', 'gex_median_genes_per_cell', 'gex_percent_duplicates', 'gex_q30_bases_in_umi', 'gex_q30_bases_in_barcode', 'gex_q30_bases_in_read_2', 'gex_q30_bases_in_sample_index_i1', 'gex_q30_bases_in_sample_index_i2', 'gex_reads_mapped_antisense_to_gene', 'gex_reads_mapped_confidently_to_exonic_regions', 'gex_reads_mapped_confidently_to_genome', 'gex_reads_mapped_confidently_to_intergenic_regions', 'gex_reads_mapped_confidently_to_intronic_regions', 'gex_reads_mapped_confidently_to_transcriptome', 'gex_reads_mapped_to_genome', 'gex_reads_with_tso', 'gex_sequenced_read_pairs', 'gex_total_genes_detected', 'gex_valid_umis', 'gex_valid_barcodes', 'total_counts', 'total_genes', 'doublet_score', 'organism_sci', 'accession_group', 'embedding_set', 'CL:ID_group', 'tokens_group', 'display_order_group', 'literature_support', 'literature_name_short', 'literature_name_long', 'curated_markers', 'color_hex_group', 'color_group', 'accession_subclass', 'CL:ID_subclass', 'tokens_subclass', 'display_order_subclass', 'color_hex_subclass', 'color_subclass', 'accession_class', 'CL:ID_class', 'tokens_class', 'display_order_class', 'color_hex_class', 'color_class', 'accession_neighborhood', 'CL:ID_neighborhood', 'tokens_neighborhood', 'display_order_neighborhood', 'color_hex_neighborhood', 'color_neighborhood', 'cell_barcode', 'barcoded_cell_sample_label', 'alignment_job_database'
    var: 'gene_id', 'gene_name', 'feature', 'chromosome', 'start', 'stop', 'n_cells_by_counts', 'mean_counts', 'log1p_mean_counts', 'pct_dropout_by_counts', 'total_counts', 'log1p_total_counts', 'mt', 'highly_variable', 'highly_variable_rank', 'means', 'variances', 'variances_norm', 'highly_variable_nbatches', 'ensembl_id'
    uns: 'AIT117_MapMyCells_Flat_Subclass_label_colors', 'AIT117_MapMyCells_Group_label_colors', 'AIT117_MapMyCells_Subclass_label_colors', 'AIT193_MapMyCells_Flat_Subclass_label_colors', 'AIT193_MapMyCells_Neighborhood_label_colors', 'AIT193_MapMyCells_Subclass_label_colors', 'batch_condition', 'cluster_algorithm', 'cluster_info', 'dataset_purl', 'default_embedding', 'filter', 'gene_annotation_version', 'hierarchy', 'hvg', 'leiden_scVI', 'log1p', 'mode', 'neighbors', 'qc_constraints', 'qc_filtered', 'reference_genome', 'schema_version', 'title', 'umap'
    obsm: 'X_scVI', 'X_umap'
    obsp: 'connectivities', 'distances'
    layers: None (.X)