. |-2020_03_27_Chen_Data |-Brg_ChIP-seq |-TEAD4_overexpression_RNAseq |---Theunissen_s5151_MGI0662 |-----Reads |-Theunissen_2965_2 |---Reads |-Theunissen_3022_78 |---Reads |-Theunissen_3031_8 |---Reads |-Theunissen_AN_C_T_2020-06-30 |---Theunissen_MGI0200 |-Theunissen_BRG_KO_ATAC |---1128 |---D0-BRG1-ATAC |---ThorATAC-mix2 |-----needmerge |---wangftp.wustl.edu |-----cfan |-------others |---------brg1 |-----------lodge |-------------fastq |-----------sth |-------------fastq |-----yliang |-------share |---------atac-seq_keratinocyte_TaRGET_pipe |---WangT_Thor |-----Processed_WangT_Thor-AN-1-ATAC_SIC803_CTCCTACAAA_S4_R1_001 |-------QC_ATAC_data_collection_WangT_Thor-AN-1-ATAC_SIC803_CTCCTACAAA_S4_R1_001 |---------plots_collection_WangT_Thor-AN-1-ATAC_SIC803_CTCCTACAAA_S4_R1_001 |---------saturation_WangT_Thor-AN-1-ATAC_SIC803_CTCCTACAAA_S4_R1_001 |---------step1.1_trimed_WangT_Thor-AN-1-ATAC_SIC803_CTCCTACAAA_S4_R1_001_1_fastqc |---------step1.1_trimed_WangT_Thor-AN-1-ATAC_SIC803_CTCCTACAAA_S4_R1_001_2_fastqc |-------step4.6_multiqc_data |-----Processed_WangT_Thor-AN-2-ATAC_SIC804_GGTCAATTAA_S5_R1_001 |-------QC_ATAC_data_collection_WangT_Thor-AN-2-ATAC_SIC804_GGTCAATTAA_S5_R1_001 |---------plots_collection_WangT_Thor-AN-2-ATAC_SIC804_GGTCAATTAA_S5_R1_001 |---------saturation_WangT_Thor-AN-2-ATAC_SIC804_GGTCAATTAA_S5_R1_001 |---------step1.1_trimed_WangT_Thor-AN-2-ATAC_SIC804_GGTCAATTAA_S5_R1_001_1_fastqc |---------step1.1_trimed_WangT_Thor-AN-2-ATAC_SIC804_GGTCAATTAA_S5_R1_001_2_fastqc |-------step4.6_multiqc_data |-----Processed_WangT_Thor-H9-1-ATAC_SIC801_CGTGGGTTCA_S2_R1_001 |-------QC_ATAC_data_collection_WangT_Thor-H9-1-ATAC_SIC801_CGTGGGTTCA_S2_R1_001 |---------plots_collection_WangT_Thor-H9-1-ATAC_SIC801_CGTGGGTTCA_S2_R1_001 |---------saturation_WangT_Thor-H9-1-ATAC_SIC801_CGTGGGTTCA_S2_R1_001 |---------step1.1_trimed_WangT_Thor-H9-1-ATAC_SIC801_CGTGGGTTCA_S2_R1_001_1_fastqc |---------step1.1_trimed_WangT_Thor-H9-1-ATAC_SIC801_CGTGGGTTCA_S2_R1_001_2_fastqc |-------step4.6_multiqc_data |-----Processed_WangT_Thor-H9-2-ATAC_SIC802_CCTAGCTGGA_S3_R1_001 |-------QC_ATAC_data_collection_WangT_Thor-H9-2-ATAC_SIC802_CCTAGCTGGA_S3_R1_001 |---------plots_collection_WangT_Thor-H9-2-ATAC_SIC802_CCTAGCTGGA_S3_R1_001 |---------saturation_WangT_Thor-H9-2-ATAC_SIC802_CCTAGCTGGA_S3_R1_001 |---------step1.1_trimed_WangT_Thor-H9-2-ATAC_SIC802_CCTAGCTGGA_S3_R1_001_1_fastqc |---------step1.1_trimed_WangT_Thor-H9-2-ATAC_SIC802_CCTAGCTGGA_S3_R1_001_2_fastqc |-------step4.6_multiqc_data |-Theunissen_BRG_reprime_part2 |---Theunissen_s5143_MGI0671 |-----Reads |-Theunissen_BRG_SNF2L_SOX2_BRM_BAF155_ChIP |---usftp21.novogene.com |-----raw_data |-------C1 |-------C1_input |-------C2 |-------C2_input |-------RZ0929_1 |-------RZ0929_10 |-------RZ0929_11 |-------RZ0929_12 |-------RZ0929_2 |-------RZ0929_3 |-------RZ0929_4 |-------RZ0929_5 |-------RZ0929_6 |-------RZ0929_7 |-------RZ0929_8 |-------RZ0929_9 |-------Undetermined |-------XH117 |-------XH118 |-------XH119 |-------XH120 |-------XH121 |-------XH122 |-------XH123 |-------XH124 |-------XH128 |-------XH129 |-------XH130 |-------XH131 |-------XH132 |-------XH133 |-------XH134 |-------XH135 |-------XH137 |-------XH138 |-Theunissen_ChIP_H3K27Ac_H3K27me3_naive_TSC |---Kroll_MGI0243 |-Theunissen_Cut_And_Tag_2020_04_02 |---Theunissen_MGI0102 |-Theunissen_hTSC_YAP_CnR |---Theunissen_MGI0239 |-Theunissen_Jan31_2020 |-Theunissen_naive_TEAD4_KD_RNAseq |---Theunissen_s5037_MGI0464 |-----Reads |-Theunissen_naive_YAP_CnR |---Theunissen_MGI0244 |-Theunissen_NR2F2_C_T |---Theunissen_MGI0578 |-Theunissen_Oct12_2021 |---atac |---RNAseq |-----Theunissen_s5578_MGI2289 |-------ALIGNED_BAM_FILES |-------QC_FILES |-------RAW_FASTQ_FILES |-------RAW_GENE_EXPRESSION_FILES |-------RAW_ISOFORM_EXPRESSION_FILES |-------Theunissen_gene-level_eXpresso |---------group_a6 |-----------group_a6_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_a6_GAGE_MSigDb_Cancer_Modules_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_a6_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_a6_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_a6_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_a6_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_a6_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_a6_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_a6_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_a6_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_a6_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_a6_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_a6_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_a6.GO_Biological_Process_Results |-----------group_a6.GO_Molecular_Function_Results |-----------group_a6.KEGG_Signaling_and_Metabolism_Results |---------group_b5 |-----------group_b5_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_b5_GAGE_MSigDb_Cancer_Modules_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_b5_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_b5_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_b5_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_b5_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_b5.GO_Biological_Process_Results |-----------group_b5.GO_Molecular_Function_Results |-----------group_b5.KEGG_Signaling_and_Metabolism_Results |---------group_d4 |-----------group_d4_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_d4_GAGE_MSigDb_Cancer_Modules_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_d4_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_d4_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_d4_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_d4_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_d4.GO_Biological_Process_Results |-----------group_d4.GO_Molecular_Function_Results |-----------group_d4.KEGG_Signaling_and_Metabolism_Results |-------Theunissen_isoform-level_eXpresso |---------group_a6 |-----------group_a6_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_a6_GAGE_MSigDb_Cancer_Modules_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_a6_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_a6_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_a6_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_a6_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_a6_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_a6_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_a6_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_a6_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_a6_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_a6_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_a6_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_a6.GO_Biological_Process_Results |-----------group_a6.GO_Molecular_Function_Results |-----------group_a6.KEGG_Signaling_and_Metabolism_Results |---------group_b5 |-----------group_b5_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_b5_GAGE_MSigDb_Cancer_Modules_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_b5_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_b5_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_b5_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_b5_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_b5.GO_Biological_Process_Results |-----------group_b5.GO_Molecular_Function_Results |-----------group_b5.KEGG_Signaling_and_Metabolism_Results |---------group_d4 |-----------group_d4_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_d4_GAGE_MSigDb_Cancer_Modules_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_d4_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_d4_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_d4_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_d4_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_d4.GO_Biological_Process_Results |-----------group_d4.GO_Molecular_Function_Results |-----------group_d4.KEGG_Signaling_and_Metabolism_Results |-----Theunissen_s5588_MGI2299 |-------ALIGNED_BAM_FILES |-------QC_FILES |-------RAW_FASTQ_FILES |-------RAW_GENE_EXPRESSION_FILES |-------RAW_ISOFORM_EXPRESSION_FILES |-------Theunissen_gene-level_eXpresso |---------group_a6 |-----------group_a6_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_a6_GAGE_MSigDb_Cancer_Modules_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_a6_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_a6_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_a6_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_a6_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_a6_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_a6_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_a6_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_a6_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_a6_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_a6_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_a6_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_a6.GO_Biological_Process_Results |-----------group_a6.GO_Molecular_Function_Results |-----------group_a6.KEGG_Signaling_and_Metabolism_Results |---------group_b5 |-----------group_b5_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_b5_GAGE_MSigDb_Cancer_Modules_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_b5_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_b5_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_b5_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_b5_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_b5.GO_Biological_Process_Results |-----------group_b5.GO_Molecular_Function_Results |-----------group_b5.KEGG_Signaling_and_Metabolism_Results |---------group_d4 |-----------group_d4_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_d4_GAGE_MSigDb_Cancer_Modules_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_d4_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_d4_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_d4_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_d4_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_d4.GO_Biological_Process_Results |-----------group_d4.GO_Molecular_Function_Results |-----------group_d4.KEGG_Signaling_and_Metabolism_Results |---------WGCNA |-----------black |-----------blue |-----------brown |-----------brown4 |-----------cyan |-----------darkgreen |-----------darkgrey |-----------darkmagenta |-----------darkolivegreen |-----------darkorange |-----------darkorange2 |-----------darkred |-----------darkturquoise |-----------floralwhite |-----------green |-----------greenyellow |-----------grey |-----------grey60 |-----------ivory |-----------lightcyan |-----------lightcyan1 |-----------lightgreen |-----------lightsteelblue1 |-----------lightyellow |-----------magenta |-----------mediumpurple3 |-----------midnightblue |-----------orange |-----------orangered4 |-----------paleturquoise |-----------pink |-----------plum1 |-----------purple |-----------red |-----------royalblue |-----------saddlebrown |-----------salmon |-----------sienna3 |-----------skyblue |-----------skyblue3 |-----------steelblue |-----------tan |-----------turquoise |-----------violet |-----------white |-----------yellow |-----------yellowgreen |-------Theunissen_isoform-level_eXpresso |---------group_a6 |-----------group_a6_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_a6_GAGE_MSigDb_Cancer_Modules_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_a6_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_a6_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_a6_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_a6_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_a6_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_a6_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_a6_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_a6_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_a6_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_a6_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_a6_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_a6.GO_Biological_Process_Results |-----------group_a6.GO_Molecular_Function_Results |-----------group_a6.KEGG_Signaling_and_Metabolism_Results |---------group_b5 |-----------group_b5_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_b5_GAGE_MSigDb_Cancer_Modules_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_b5_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_b5_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_b5_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_b5_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_b5.GO_Biological_Process_Results |-----------group_b5.GO_Molecular_Function_Results |-----------group_b5.KEGG_Signaling_and_Metabolism_Results |---------group_d4 |-----------group_d4_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_d4_GAGE_MSigDb_Cancer_Modules_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_d4_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_d4_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_d4_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_d4_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_d4.GO_Biological_Process_Results |-----------group_d4.GO_Molecular_Function_Results |-----------group_d4.KEGG_Signaling_and_Metabolism_Results |-----Theunissen_s5589_MGI2302 |-------ALIGNED_BAM_FILES |-------QC_FILES |-------RAW_FASTQ_FILES |-------RAW_GENE_EXPRESSION_FILES |-------RAW_ISOFORM_EXPRESSION_FILES |-------Theunissen_gene-level_eXpresso |---------group_a6 |-----------group_a6_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_a6_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_a6_GAGE_MSigDb_Immunologic_Signatures_Results |---------group_b5 |-----------group_b5_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_b5_GAGE_MSigDb_Cancer_Modules_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_b5_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_b5_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_b5_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_b5_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_b5_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_b5_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_b5_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_b5_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_b5.GO_Biological_Process_Results |-----------group_b5.GO_Molecular_Function_Results |-----------group_b5.KEGG_Signaling_and_Metabolism_Results |---------group_d4 |-----------group_d4_GAGE_MSigDb_Cancer_Gene_Neighborhoods_Results |-----------group_d4_GAGE_MSigDb_Cancer_Modules_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Biocarta_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.KEGG_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.PID_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Reactome_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways_Results |-----------group_d4_GAGE_MSigDb_Canonical_Pathways.Wikipathways_Results |-----------group_d4_GAGE_MSigDb_Cell_Type_Signatures_Results |-----------group_d4_GAGE_MSigDb_Chemical_and_Genetic_Perturbations_Results |-----------group_d4_GAGE_MSigDb_Hallmark_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Human_Phenotype_Ontology_Results |-----------group_d4_GAGE_MSigDb_Immunologic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Legacy_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_miRDB_microRNA_Targets_Results |-----------group_d4_GAGE_MSigDb_Oncogenic_Signatures_Results |-----------group_d4_GAGE_MSigDb_Positional_Gene_Sets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_GTRD_Targets_Results |-----------group_d4_GAGE_MSigDb_Transcription_Factor_Motif_Targets_Results |-----------group_d4.GO_Biological_Process_Results |-----------group_d4.GO_Molecular_Function_Results |-----------group_d4.KEGG_Signaling_and_Metabolism_Results |---------WGCNA |-----------black |-----------blue |-----------brown |-----------cyan |-----------darkgreen |-----------darkgrey |-----------darkmagenta |-----------darkolivegreen |-----------darkorange |-----------darkred |-----------darkturquoise |-----------green |-----------greenyellow |-----------grey |-----------grey60 |-----------lightcyan |-----------lightgreen |-----------lightyellow |-----------magenta |-----------midnightblue |-----------orange |-----------paleturquoise |-----------pink |-----------purple |-----------red |-----------royalblue |-----------saddlebrown |-----------salmon |-----------sienna3 |-----------skyblue |-----------steelblue |-----------tan |-----------turquoise |-----------violet |-----------white |-----------yellow |-----------yellowgreen |-Theunissen_RNAseq_BRG_KO_SNF2L_KD_BRM |---fastq |-Theunissen_SNF2L_C_T |---Theunissen_MGI0580 |-Theunissen_TEAD1_CutandTag_H9TSC_20201217 |---Theunissen_MGI0559 |-Theunissen_TEAD4_KD_RNAseq |---Theunissen_s4963_MGI0331 |-----Reads |-Theunissen_WGBS_20190930 |-ThorATAC |---fastq |---WangT_Thor