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Info on 4DN HFF imputations
The HFFc6 cell line was incorporated as an additional cell type into the Avocado model (Schreiber et al., 2020), using data from DNase-seq, microRNA-seq, CTCF ChIP-seq and total RNA-seq assays. The model was fine tuned to estimate the corresponding cell type factor for HFFc6. Having validated that the model outperforms several baselines on imputing held-out HFFc6 assays, we further imputed all missing assay types following the Avocado framework.
A slide providing additional information is available here
Phased Genomes
Haplotype phased variant calls on 4DN cell lines
These haplotype phased variant callsets are the intersection between the callsets from GATK HaplotypeCaller and freebayes, which were performed by the Gilbert Lab on 10X Genomics linked reads from the indicated cell lines
Loop Calls
Chromatin Loop Calls on Joint Analysis Lines (H1 and HFFc6) using input from multiple complementary genomic assays
SPIN States
Predicted SPIN States on Joint Analysis Cell lines
3D Models
3D Models and structural feature calls for H1-ESC and HFFc6 cells