This website contains links and resources associated with the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency" by Nair, Ameen et al.

• scRNA Browser: Browser to explore scRNA-seq data that includes visualization of endogenous and Sendai OSKM quantification. Based on Vitessce.
• scATAC Browser: Browser to explore scATAC-seq data at cluster resolution. The signal tracks are -log p-value tracks derived from the ENCODE bulk ATAC-seq pipeline. The dynseq tracks correspond to counts SHAP interpretation from state-specific models within peaks.

• Mapped products: Aligned fragment files for scATAC-seq and multiome, and unfiltered counts matrices for scRNA-seq and multiome. Please refer to the README included. A subset of this data has also been deposited in the Gene Expression Omnibus database with the Super-Series reference number GSE242424.
• Analysis products: Includes counts matrices for scATAC-seq, scRNA-seq, and multiome integrated across all samples, cell representations, UMAP coordinates, cluster assignment. For scATAC-seq clusters, includes per cluster fragment files and peak calls. For scRNA-seq, contains endogenous and Sendai OSKM estimates.
• ChromBPNet models and data: Includes 10-fold models for each cluster in multiple formats (tf1.14, tf2.X and saved weights). Includes regions (peaks + nonpeaks) and bigwig files used for each cluster.
• Interpretation and motifs: Counts and profile importance scores, corresponding TF-MoDISco outputs, and consolidated motifs.

The code used for all analyses and for model training, evaluation and interpretation can be found here.