# Readme doc for the study "Integrative methylome-transcriptome analysis unravels cancer-cell vulnerabilities in infant MLL-rearranged B-ALL" (Datasets and additional tables) # This dataset contains information related to dataframes, databases, scripts and supplementary material mentioned in the original manuscript: ####################### # Supplemental tables # ####################### Supplemental_Table_1.xlsx Supplemental_Table_2.xlsx Supplemental_Table_3.xlsx Supplemental_Table_4.xlsx Supplemental_Table_5.xlsx Supplemental_Table_6.xlsx Supplemental_Table_7.xlsx Supplemental_Table_8.xlsx Supplemental_Table_9.xlsx Supplemental_Table_10.xlsx Supplemental_Table_11.xlsx Supplemental_Table_12.xlsx Supplemental_Table_13.xlsx Supplemental_Table_14.xlsx Supplemental_Table_15.xlsx Supplemental_Table_16.xlsx Supplemental_Table_17.xlsx Supplemental_Table_18.xlsx Supplemental_Table_19.xlsx Supplemental_Table_20.xlsx ############## # Tables.zip # ############## # Length Name # --------- ---- # 0 Tables/ # 0 Tables/Annotations/ #1141284419 Tables/Annotations/All_annotations_leukemia_background.txt # 6023986 Tables/Annotations/CD19+_EP.txt # 1131 Tables/Annotations/List_motifs_hyper_hypo_neg_pos_correlations.txt # 109480 Tables/Annotations/List_of_AF4_specific_DMPs.txt # 68175 Tables/Annotations/List_of_AF9_specific_DMPs.txt # 183565 Tables/Annotations/List_of_Bcell_specific_DMPs.txt # 85302 Tables/Annotations/List_of_GERM_specific_DMPs.txt # 200857 Tables/Annotations/List_of_leukemia_common_hypermethylated_DMPs.txt # 186744 Tables/Annotations/List_of_leukemia_common_hypomethylated_DMPs.txt # 191144795 Tables/Annotations/annotation_EPIC.txt # 6087690 Tables/Annotations/bVals_B_vs_ProB.txt # 55599 Tables/Annotations/transcription_factor_list.txt # 168594 Tables/Annotations/List of_CRISPR_FOSL2KO_DMPs.txt # 129408 Tables/Annotations/List of_CRISPR_t4:11_DMPs.txt # 0 Tables/MAE/ # 13997772 Tables/MAE/mae_AF4_filtered.rda # 11283312 Tables/MAE/mae_AF9_filtered.rda # 266461280 Tables/MAE/mae_ALL_conditions.rda # 23583512 Tables/MAE/mae_COMMON_filtered.rda # 11683292 Tables/MAE/mae_GERM_filtered.rda # 0 Tables/Motifs/ # 259461 Tables/Motifs/AF4_E2F5_motif_targets.txt # 119496 Tables/Motifs/AF4_FOSL2_motif_targets.txt # 115023 Tables/Motifs/AF4_RUNX1_motif_targets.txt # --------- ------- ------- #1673232893 3 folders 26 files ########### # src.zip # ########### # Length Name # --------- ---- # 0 src/ # 3970 src/01_WGBS_processing_Bismark.sh # 1564 src/02_generate_bismark_methylation_reports.R # 4272 src/03_generate_tiling_windows_WGBS.R # 2347 src/04_generate_violinplot_tiling_windows_WGBS.R # 51929 src/05_generate_circos.R # 21028 src/06_generate_methylation_landscape_FTL3.R # 3890 src/07_WGBS_BSseq_DMR_calculations_AF4.R # 3890 src/08_WGBS_BSseq_DMR_calculations_AF9.R # 3915 src/09_WGBS_BSseq_DMR_calculations_nonMLL.R # 4169 src/10_generate_Venn_DMRs_WGBS_leukemias.R # 2748 src/11_calculate_enrichment_repeats_WGBS.R # 6898 src/12_generate_heatmap_repeats_WGBS.R # 2093 src/13_generate_violinplot_repeats_EPIC_array.R # 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4716 src/37_Script_diff_gene_exp_Ebseq.R # 21366 src/38_generate_Ebseq_matrix_FPKM_TPM_Isoamount.R # 3636 src/39_heatmap_PCA_representation_RNAseq.R # 3601 src/40_UpSetR_plot_representation_RNAseq_data.R # 3248 src/41_calculate_cv_RNAseq_leukemias.R # 2672 src/36_Compare_GE_Meth_clusters.R # 3336 src/42_coexpression_network_CEMiTools_leukemia.R # 11047 src/43_script_methylation_elmer_createMAE.R # 4751 src/44_script_methylation_elmer_AF4_4.R # 4752 src/45_script_methylation_elmer_AF9_4.R # 4789 src/46_script_methylation_elmer_GERM_4.R # 4989 src/47_script_methylation_elmer_COMMON_4.R # 9850 src/48_calculate_correlations_infant_leukemia_4.R # 3169 src/49_enrichment_roadmap_histone_correlations.R # 5469 src/50_heatmaps_histone_leukemia_correlations.R # 10447 src/51_enrichment_roadmap_segmentation_correlations.R # 4468 src/52_heatmaps_segmentation_leukemia_correlations.R # 4149 src/53_plots_figure_correlations_infant_leukemia 4.R # 9172 src/54_Gene_ontologies_correlations.R # 10013 src/55_script_represent_correlations_meth_expression.R # 4087 src/56_represent_heatmaps_motif_enrichment.R # 18346 src/57_Represent_average_meth_TF_exp_network.R # 12159 src/58_get_betas_and DMPS_from_IDATS_CRISPR.R # 956 src/59_HOMER_motif_analysis_FOSL2KO.sh # 9252 src/62_Miscellaneous_figures.R # 3559 src/60_enrichment_GTRD_TFBS_CRISPR_t4:11exp.R # 851 src/61_calculate_expression_RSEM_CRISPR_Exp.sh # --------- ------- ------- # 425971 1 folder 63 files ############ # Data.zip # ############ # Length Name # --------- ---- # 0 Data/ # 0 Data/EPIC/ # 0 Data/RNAseq/ # 0 Data/HOMER/ # 0 Data/HOMER/Annotation_HOMER/ # 0 Data/HOMER/HOMER_output/ # 0 Data/HOMER/HOMER_output/AF4_hyper/ # 0 Data/HOMER/HOMER_output/AF4_hyper/homerResults/ # 0 Data/HOMER/HOMER_output/AF4_hyper/knownResults/ # 0 Data/HOMER/HOMER_output/AF4_hypo/ # 0 Data/HOMER/HOMER_output/AF4_hypo/homerResults/ # 0 Data/HOMER/HOMER_output/AF4_hypo/knownResults/ # 0 Data/HOMER/HOMER_output/nonMLL_hyper/ # 0 Data/HOMER/HOMER_output/nonMLL_hyper/homerResults/ # 0 Data/HOMER/HOMER_output/nonMLL_hyper/knownResults/ # 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