Designing synthetic regulatory elements using DNA-Diffusion, a generative AI framework

File: supplementary_tables.zip

Manuscript Supplementary tables a-g

Supplementary Data 1

File: JASPAR_motifs.txt.zip

Description: JASPAR MOODS  Motif Matches by Sequence ID and Cell Type in Training, Validation, Test, and Generated Sets (with Positions and Scores)

Supplementary Data 2

File: Co_occurence_motifs_JASPAR.zip

Description: MOODS Motifs Co-occurrence for Training, Test, Validation and Generated sequences separated by cell-type (GM12878, HepG2, K562)

Supplementary Data 3

File: Enformer_and_Chrombpnet_predictions_enhancer_promoters_different_loci.zip

Description: Tables containing Enformer and ChromBPNet (DNase, CAGE, H3K4me3) predictions for enhancer and genes promoter in different genomic loci.

Supplementary Data 4

File: EXTRASEQ_counts.tab.zip

Description: EXTRA-Seq barcode raw counts for mRNA and DNA for five different replicates

Supplementary Data 5

File: DNA-Diffusion.pt

DNA-Diffusion PyTorch weights  (see: https://github.com/pinellolab/DNA-Diffusion ) 

Supplementary Data 6

File: mpra_model_best-epoch_07_val_MalinoisMPRA_mean_SpearmanR_0_73185.ckpt

Weights of the predictor MPRA model trained with the Malinois MPRA data.

Supplementary Data 7

File: DeepMEL_training.zip

Weights and code to train and sample deepMEL trained in  the DHS index data for GM12878, K562, and GM12878

Supplementary Data 8

File: wgan_training.zip

Weights and code to train the different WGAN in different cell types. DeepMEL was trained in  the DHS index data. One model per cell:  GM12878, K562, and GM12878

Supplementary Data 9

File: CODA_training.zip

Weights and code to train and sample CODA trained in the DHS index data for GM12878, K562, and GM12878

Supplementary Data 10

File: EXTRASEQ_AND_STARRSEQ_R_mpra_voom_scripts.zip

Scripts to process EXTRA-Seq and STARR-Seq data from DNA and mRNA counts used to compute the  mRNA/DNA log fold change using the different experiment replicates.

Supplementary Data 11

File: DNA-Diffusion-0.0.2.zip

DNA-Diffusion library source code

Supplementary Data 12

MPRA_predictions.txt

MPRA predictions for the different cell types