Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT

Figure 2:

1) CRC_outcome.csv: Outcome annotation of TACIT, CELESTA, SCINA, and Louvain using CRC datasets

2) HI_outcome.csv: Outcome annotation of TACIT, CELESTA, SCINA, and Louvain using HI datasets

3) Signature_CRC_Celesta.csv: signature matrix use for CELESTA in CRC datasets

4) Signature_CRC_TACIT_SCINA_Louvain.csv: signature matrix use for TACIT, SCINA, and Louvain in CRC datasets

5) Signature_HI_Celesta.csv: signature matrix use for CELESTA in HI datasets

6) Signature_HI_TACIT_SCINA_Louvain.csv: signature matrix use for TACIT, SCINA, and Louvain in HI datasets

Figure 3:

1) cluster_proportions_scRNA.csv: Proportion of cell type in scRNA

2) Signature_Xenium_TACIT_Louvain: signature matrix use for Xenium-SjD datasets

3) result_TACIT_Xenium1_5_merge.csv: Outcome annotation of TACIT, Louvain, Seurat transfer, and Louvain using Xenium-SjD dataset 

Figure 4:

1) Signature_PCF_Figure_4.csv: signature matrix use for PCF pair datasets

2) Signature_Xenium_TACIT_Louvain.csv: signature matrix use for Xenium pair datasets (same with Figure 3)

3) data_final_combine_PCF.csv: data expression and annotation in pair PCF-Xenium

4) data_final_combine_Xenium.csv: data expression and annotation in pair PCF-Xenium

Figure 5:

1) Signature_PCF_Figure_4.csv: signature matrix use for PCF pair datasets

2) Signature_Xenium_TACIT_Louvain.csv: signature matrix use for Xenium pair datasets (same with Figure 3)

3) data_final_combine_PCF.csv: data expression and annotation in pair PCF-Xenium

4) data_final_combine_Xenium.csv: data expression and annotation in pair PCF-Xenium

Figure 6:

1) PCF_Xenium_reg001.csv: pair Xenium-PCF with annotation

2) PCF_Xenium_reg002.csv: pair Xenium-PCF with annotation

3) PCF_Xenium_reg003.csv: pair Xenium-PCF with annotation

4) PCF_Xenium_reg004.csv: pair Xenium-PCF with annotation

5) PCF_Xenium_reg005.csv: pair Xenium-PCF with annotation

6) PCF_Xenium_reg006.csv: pair Xenium-PCF with annotation

7) Signature_PCF_figure6.csv: match signature in PCF

8) Signature_Xenium_figure6.csv: match signature in Xenium

9) Signature_PCF_Xenium_Figure6.csv: combine signature in PCF and Xenium

Acknowledgements:

This work was supported by generous start-up funds from the ADA Science & Research Institute (Volpe Research Scholar Award) and the Chan Zuckerberg Initiative/Foundation program Pediatric Networks for the Human Cell Atlas to KMB. The work also benefited from the VCU Wright Regional Center for Clinical & Translational Science (CCTS) Clinical and Translational Science Award (CTSA) UM1TR004360 to JL and NIH-NCI Cancer Center Support Grant P30 CA016059 to JL and KMT.