Published February 19, 2024 | Version v1
Dataset Open

Spatial mapping of human hematopoiesis at single-cell resolution reveals aging-associated topographic remodeling

  • 1. BostonGene
  • 2. ROR icon Weill Cornell Medicine
  • 3. ROR icon NewYork–Presbyterian Hospital

Description

This repository contains the data for the paper "Spatial mapping of human hematopoiesis at single-cell resolution reveals aging-associated topographic remodeling".

Data schema is follows:

'n_obs': 1510295,
 'n_vars': 6,
 'obs': ['sample_id',
         'cell_index',
         'cell_type',
         'graph_cluster',
         'distance_Fat',
         'distance_Trabecules',
         'distance_Endothelium',
         'perimeter',
         'center_x',
         'center_y',
         'cell_type_community',
         'nb_num_pixels_150_Endothelium',
         'nb_num_pixels_150_Trabeculae',
         'nb_num_pixels_150_Fat',
         'nuclei_ratio',
         'case_id',
         'category',
         'age_at_dx',
         'm_f',
         'CD71_mean_intensity',
         'CD61_mean_intensity',
         'CD117_mean_intensity',
         'CD38_mean_intensity',
         'CD34_mean_intensity',
         'CD15_mean_intensity',
         'chm',
         'cell_area_um',
         'age_group',
         'gender',
         'fat_to_cell_ratio',
         'fat_to_cell_amount',
         'organism_ontology_term_id',
         'donor_id',
         'disease_ontology_term_id',
         'tissue_type',
         'suspension_type',
         'development_stage_ontology_term_id',
         'sex_ontology_term_id',
         'assay_ontology_term_id',
         'tissue_ontology_term_id',
         'self_reported_ethnicity_ontology_term_id',
         'cell_type_ontology_term_id'],
 'obsm': ['X_graph_nn_embeddings', 'X_pca', 'spatial'],
 'uns': ['age_group_palette',
         'cell_type_colors',
         'cell_type_order',
         'cell_type_palette',
         'cytopenia_palette',
         'dendrogram_graph_cluster',
         'gender_palette',
         'graph_cluster_palette',
         'sample_order',
         'staging_palette',
         'tissue_type_palette',
         'title'],
 'var': ['gene_name_at_imaging']}

 

anndata.X contains mean intensity values per segmented cell contour

Files

Files (841.4 MB)

Name Size Download all
md5:bbcadd10d53e23255f285278bf050d73
841.4 MB Download

Additional details

Software

Repository URL
https://github.com/BostonGene/AgingHemaTopoMap
Development Status
Wip