inferring cellular communication through mapping cells in space using Tangram 2 | Reproducibility Dataset

This record provides the data artifacts that support Huang et al., 2025, “Inferring cellular communication through mapping cells in space using Tangram 2” (preprint: https://doi.org/10.1101/2025.09.28.679077). It includes real and simulated single-cell and spatial transcriptomics resources used to reproduce the figures and results in the paper.

Contents

Curated inputs from publicly available single-cell and spatial datasets (referenced by their original repository DOIs/accessions).

Tangram 2 analysis outputs required to regenerate the main and extended figures (e.g., preprocessed matrices, mappings, interaction/communication scores, and figure-level source data tables).

Simulation configurations, seeds, and generated synthetic datasets used for benchmarks and ablations.

Data sources (public inputs)No new primary human-subject data were collected. Public datasets used in this study include:

Slide-tags tonsil snRNA-seq (Broad SCP2169): https://singlecell.broadinstitute.org/single_cell/study/SCP2169/slide-tags-snrna-seq-on-human-tonsil

Cell cultures (GEO GSE135382): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135382

Colon collection (CELLxGENE): https://cellxgene.cziscience.com/collections/4fa07e63-f712-4d8c-b885-2c515b5e2743

Lymph node (10x Visium): https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Human_Lymph_Node

Lymphoid scRNA-seq (cell2location): https://cell2location.cog.sanger.ac.uk/paper/integrated_lymphoid_organ_scrna/RegressionNBV4Torch_57covariates_73260cells_10237genes/sc.h5ad

Cutaneous squamous cell carcinoma (GEO GSE144240): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144240

Breast cancer atlas (Zenodo 4739739): https://zenodo.org/records/4739739

TCGA Lung Squamous Cell Carcinoma (cBioPortal): https://www.cbioportal.org/study/summary?id=lusc_tcga_pan_can_atlas_2018

TCGA Head & Neck Squamous Cell Carcinoma (cBioPortal): https://www.cbioportal.org/study/summary?id=hnsc_tcga_pan_can_atlas_2018

TCGA Skin Cutaneous Melanoma (cBioPortal): https://www.cbioportal.org/study/summary?id=skcm_tcga_pan_can_atlas_2018

Breast dataset (CELLxGENE): https://cellxgene.cziscience.com/e/9fddb063-056d-4202-8b8a-4b0ee531d3ce.cxg/

Reproducibility

The analysis code and exact workflow to regenerate all results are available at: https://github.com/Genentech/tangram2. Environment files and step-by-step instructions are provided there.