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  • Supplementary figures: Fig. S1: Gene names for the data shown in Fig. 1aâ c, Fig. S2: Transcription factor motifs enriched in top ChIP-seq and ATAC-seq regions, Fig. S3: Differential H3K27ac analysis of ATAC-seq regions is an effective method to identify tissue-specific enhancers, Fig. S4: Genes near putative ATAC-seq derived enhancers are differentially regulated across tissues, Fig. S5: The identified putative DV enhancer regions derived from ATAC-seq are enriched for known DV transcription factor motifs, Fig. S6: Number of genes with one or multiple assigned enhancers, Fig. S7: Transcription factor ChIP-seq signal is preferentially found at the expected corresponding binding motifs present within putative MEs and DEEs. (PDF 2673 kb)
    Data Types:
    • Document
  • Supplementary material: Includes references for known DV enhancers, ChIP-seq and ATAC-seq replicate correlations, and an overview of how some known DV enhancers were assigned to potential target genes. (DOCX 3548 kb)
    Data Types:
    • Document
  • Supplementary material: Includes references for known DV enhancers, ChIP-seq and ATAC-seq replicate correlations, and an overview of how some known DV enhancers were assigned to potential target genes. (DOCX 3548 kb)
    Data Types:
    • Document
  • Supplementary figures: Fig. S1: Gene names for the data shown in Fig. 1aâ c, Fig. S2: Transcription factor motifs enriched in top ChIP-seq and ATAC-seq regions, Fig. S3: Differential H3K27ac analysis of ATAC-seq regions is an effective method to identify tissue-specific enhancers, Fig. S4: Genes near putative ATAC-seq derived enhancers are differentially regulated across tissues, Fig. S5: The identified putative DV enhancer regions derived from ATAC-seq are enriched for known DV transcription factor motifs, Fig. S6: Number of genes with one or multiple assigned enhancers, Fig. S7: Transcription factor ChIP-seq signal is preferentially found at the expected corresponding binding motifs present within putative MEs and DEEs. (PDF 2673 kb)
    Data Types:
    • Document
  • Replicate concordance for ChIP-seq for various histone modifications. ChIP-seq replicate concordance is shown with Pearsonâ s correlation coefficient (r-values) calculated on Log (1â +â ngs.plot) enrichment values for all six histone marks. (PDF 7315 kb)
    Data Types:
    • Document
  • Replicate concordance for ChIP-seq for various histone modifications. ChIP-seq replicate concordance is shown with Pearsonâ s correlation coefficient (r-values) calculated on Log (1â +â ngs.plot) enrichment values for all six histone marks. (PDF 7315 kb)
    Data Types:
    • Document
  • Additional file 2: Figure S1. Comparison of ChIP results in SuUR mutants and in wild type obtained with H3K27me3 antibodies from different vendors and with the antibodies against H3K27me2. A—scatter plot of ChIP-chip signals obtained with the Abcam #6002 antibodies in SuUR mutants (abscissa) and in wild type (ordinate) [13]. B—scatter plot showing H3K27me3 ChIP-seq signals obtained with Cell Signaling Technology #9733 (CST #9733) antibodies in the same genotypes. C—the same analysis performed with Millipore #07-452 antibodies against H3K27me2. Datapoints inside 193 SSRs are shown in red. In both cases (A and B) H3K27me3 antibodies produce the characteristic skew (arrows): SSRs systematically show stronger signal in wild type strain as compared to SuUR mutants. This tendency is absent in case of H3K27me2 (C).
    Data Types:
    • Document
  • Distribution of lncRNA types in the different euchromatin regions. Figure S2. Occupied regions for each chromatin signature. Table S1. The length of lncRNAs. Table S2. RNA-seq datasets. Table S3. Statistics of exon numbers in lncRNA and mRNA genes from different sources. Table S4. Raw Ct values of RT-qPCR experiments for un-transcribed regions and the selected lncRNAs. Table S5. ChIP-seq datasets. Table S6. The primer list of the selected lncRNAs for RT-qPCR experiments. (PDF 356 kb)
    Data Types:
    • Document
  • Distribution of lncRNA types in the different euchromatin regions. Figure S2. Occupied regions for each chromatin signature. Table S1. The length of lncRNAs. Table S2. RNA-seq datasets. Table S3. Statistics of exon numbers in lncRNA and mRNA genes from different sources. Table S4. Raw Ct values of RT-qPCR experiments for un-transcribed regions and the selected lncRNAs. Table S5. ChIP-seq datasets. Table S6. The primer list of the selected lncRNAs for RT-qPCR experiments. (PDF 356 kb)
    Data Types:
    • Document
  • Additional file 1: Figure S1. dCTCF and CP190 peaks co-localize with previously identified dCTCF and CP190 binding sites. Peaks for dCTCF and CP190 were identified using MACS2 based on publicly available (GSE41354) ChIP-seq profiles published in Ong et al. [42] (PMID 24055367). Average binding of dCTCF as well as CP190 before and after expression of FLAG-dSUMO is shown across the known dCTCF (left) and CP190 (right) binding sites.
    Data Types:
    • Document