Characterizing cell-type spatial relationships across length scales in spatially resolved omics data: data repository

CRAWDAD

Spatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of such technologies offers the opportunity to delineate cell-type spatial relationships, particularly across different length scales, and enhance our understanding of tissue organization and function. To quantify such multi-scale cell-type spatial relationships, we develop CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package with source code and additional documentation at https://jef.works/CRAWDAD/.

During CRAWDAD's development, we generated simulated datasets and new cell-type annotations for human spleen data, provided here. The external datasets such as the mouse cerebellum, mouse embryo, mouse brain, and human breast cancer data used in the paper can be found in their original publication. See more information in CRAWDAD's data availability statement.

Simulated Datasets

sim.csv: the simulated data. Used in Figure 1 b-g, Supplementary Figure 1 a-c, and Supplementary Figure 9 a-b.

ext_sim.csv: the extended simulated data. Used in Supplementary Figure 1 d-f.

null_sim_visualization.csv: the null simulated data. Used to generate the plots Supplementary Figure 2 a-d.

null_sim_1.csv - null_sim_10.csv: the 10 null simulated datasets. Used to quantitatively compare CRAWDAD, Squidpy’s co-occurrence implementation, and Ripley’s K Cross.

HuBMAP Datasets

pkhl.csv: annotated cell types and positions of sample HBM389.PKHL.936 from donor HBM966.VNKN.965. Used in Figure 5 a-h, Supplementary Figure 5 a, Supplementary Figure 7 a-c, and Supplementary Figure 8 c. doi:10.35079/HBM389.PKHL.936

xxcd.csv: annotated cell types and positions of sample HBM772.XXCD.697 from donor HBM966.VNKN.965. Used in Figure 5 d-h, Supplementary Figure 5 a-c, and Supplementary Figure 7 a-c. doi:10.35079/HBM772.XXCD.697

fsld.csv: annotated cell types and positions of sample HBM342.FSLD.938 from donor HBM245.ZWNT.288. Used in Figure 5 e-f, h, Supplementary Figure 5 a-c, Supplementary Figure 6 a-b, and Supplementary Figure 7 a-c. doi:10.35079/HBM342.FSLD.938

pbvn.csv: annotated cell types and positions of sample HBM825.PBVN.284 from donor HBM245.ZWNT.288. Used in Figure 5 e-f, h, Supplementary Figure 5 a-c, Supplementary Figure 6 a-b, and Supplementary Figure 7 a-c. doi:10.35079/HBM825.PBVN.284

ksfb.csv: annotated cell types and positions of sample HBM556.KSFB.592 from donor HBM298.KGNJ.374. Used in Figure 5 e-f, h, Supplementary Figure 5 a-c, Supplementary Figure 6 a-b, and Supplementary Figure 7 a-c. doi:10.35079/HBM556.KSFB.592

ngpl.csv: annotated cell types and positions of sample HBM568.NGPL.345 from donor HBM298.KGNJ.374. Used in Figure 5 e-f, h, Supplementary Figure 5 a-c, Supplementary Figure 6 a-b, and Supplementary Figure 7 a-c. doi:10.35079/HBM568.NGPL.345

External Datasets

Mouse cerebellum: Used in Figure 2 a-e, Supplementary Figure 3 a-b, Supplementary Figure 4 a-d, and Supplementary Figure 8 a.

Mouse embryo: Used in Figure 2 f-j, Supplementary Figure 3 c-d, Supplementary Figure 4 e-h, and Supplementary Figure 8 b.

Human breast cancer: Used in Figure 3 a-c.

Mouse brains: Used in Figure 4 a-e.