SRX5101691 GSM3504370 SRP172770 SRS4111933 GSM3504370 ATAC-seq GENOMIC other Approximately 50,000 bead-bound PCM-1(+) CM nuclei were used as input for the assay for transposase accessible chromatin with high throughout sequencing (ATAC-seq). ATAC-seq libraries were generated as previously described (Buenrostro et al., 2013). Paired end 2x75 bp sequencing was performed with an Illumina Nextseq instrument (DNA Link Inc.). Reads were mapped to the mouse genome (mm10) by using Bowtie2 with default paired-end settings (Langmead et al., 2009). Next, all non-nuclear reads and improperly paired reads were discarded. Duplicated reads were removed with Picard-1174 MarkDuplicates. Peak calling was carried out with MACS2 (callpeak–nomodel–broad). Blacklisted regions were lifted over from mm9 to mouse genome mm10 and removed along with peaks of low sequencing quality (>q30 required). Reads were counted for each condition from the comprehensive peak file (YAP5SA OE and control replicates merged) by using bedtools (multicov module) (Quinlan, 2014). Quantile normalization of ATAC-seq data sets was performed with CQN (Hansen et al., 2012), and offsets were fed into DESeq2 to quantify differential accessibility (Love et al., 2014). Nucleosome calling was carried out with NucleoATAC (Schep et al., 2015). Motif enrichment analysis was conducted with HOMER (Heinz et al., 2010) (findMotifsGenome.pl and annotatePeaks.pl). Gene tracks were shown by using the UCSC genome browser. ES cell ATAC-seq data was used from GSM1563569, with reads mapped to the mm10 genome using bowtie2 and analyzed with HOMER (annotatePeaks.pl) and Galaxy/deeptools2 (multiBigwigSummary, plotCorrelation) (Ramirez et al., 2016). NextSeq 500 gds 303504370 GSM3504370 GEO Accession GSM3504370 SRX5101692 GSM3504371 SRP172770 SRS4111934 GSM3504371 ATAC-seq GENOMIC other Approximately 50,000 bead-bound PCM-1(+) CM nuclei were used as input for the assay for transposase accessible chromatin with high throughout sequencing (ATAC-seq). ATAC-seq libraries were generated as previously described (Buenrostro et al., 2013). Paired end 2x75 bp sequencing was performed with an Illumina Nextseq instrument (DNA Link Inc.). Reads were mapped to the mouse genome (mm10) by using Bowtie2 with default paired-end settings (Langmead et al., 2009). Next, all non-nuclear reads and improperly paired reads were discarded. Duplicated reads were removed with Picard-1174 MarkDuplicates. Peak calling was carried out with MACS2 (callpeak–nomodel–broad). Blacklisted regions were lifted over from mm9 to mouse genome mm10 and removed along with peaks of low sequencing quality (>q30 required). Reads were counted for each condition from the comprehensive peak file (YAP5SA OE and control replicates merged) by using bedtools (multicov module) (Quinlan, 2014). Quantile normalization of ATAC-seq data sets was performed with CQN (Hansen et al., 2012), and offsets were fed into DESeq2 to quantify differential accessibility (Love et al., 2014). Nucleosome calling was carried out with NucleoATAC (Schep et al., 2015). Motif enrichment analysis was conducted with HOMER (Heinz et al., 2010) (findMotifsGenome.pl and annotatePeaks.pl). Gene tracks were shown by using the UCSC genome browser. ES cell ATAC-seq data was used from GSM1563569, with reads mapped to the mm10 genome using bowtie2 and analyzed with HOMER (annotatePeaks.pl) and Galaxy/deeptools2 (multiBigwigSummary, plotCorrelation) (Ramirez et al., 2016). NextSeq 500 gds 303504371 GSM3504371 GEO Accession GSM3504371 SRX5101693 GSM3504372 SRP172770 SRS4111935 GSM3504372 ATAC-seq GENOMIC other Approximately 50,000 bead-bound PCM-1(+) CM nuclei were used as input for the assay for transposase accessible chromatin with high throughout sequencing (ATAC-seq). ATAC-seq libraries were generated as previously described (Buenrostro et al., 2013). Paired end 2x75 bp sequencing was performed with an Illumina Nextseq instrument (DNA Link Inc.). Reads were mapped to the mouse genome (mm10) by using Bowtie2 with default paired-end settings (Langmead et al., 2009). Next, all non-nuclear reads and improperly paired reads were discarded. Duplicated reads were removed with Picard-1174 MarkDuplicates. Peak calling was carried out with MACS2 (callpeak–nomodel–broad). Blacklisted regions were lifted over from mm9 to mouse genome mm10 and removed along with peaks of low sequencing quality (>q30 required). Reads were counted for each condition from the comprehensive peak file (YAP5SA OE and control replicates merged) by using bedtools (multicov module) (Quinlan, 2014). Quantile normalization of ATAC-seq data sets was performed with CQN (Hansen et al., 2012), and offsets were fed into DESeq2 to quantify differential accessibility (Love et al., 2014). Nucleosome calling was carried out with NucleoATAC (Schep et al., 2015). Motif enrichment analysis was conducted with HOMER (Heinz et al., 2010) (findMotifsGenome.pl and annotatePeaks.pl). Gene tracks were shown by using the UCSC genome browser. ES cell ATAC-seq data was used from GSM1563569, with reads mapped to the mm10 genome using bowtie2 and analyzed with HOMER (annotatePeaks.pl) and Galaxy/deeptools2 (multiBigwigSummary, plotCorrelation) (Ramirez et al., 2016). NextSeq 500 gds 303504372 GSM3504372 GEO Accession GSM3504372 SRX5101694 GSM3504373 SRP172770 SRS4111936 GSM3504373 ATAC-seq GENOMIC other Approximately 50,000 bead-bound PCM-1(+) CM nuclei were used as input for the assay for transposase accessible chromatin with high throughout sequencing (ATAC-seq). ATAC-seq libraries were generated as previously described (Buenrostro et al., 2013). Paired end 2x75 bp sequencing was performed with an Illumina Nextseq instrument (DNA Link Inc.). Reads were mapped to the mouse genome (mm10) by using Bowtie2 with default paired-end settings (Langmead et al., 2009). Next, all non-nuclear reads and improperly paired reads were discarded. Duplicated reads were removed with Picard-1174 MarkDuplicates. Peak calling was carried out with MACS2 (callpeak–nomodel–broad). Blacklisted regions were lifted over from mm9 to mouse genome mm10 and removed along with peaks of low sequencing quality (>q30 required). Reads were counted for each condition from the comprehensive peak file (YAP5SA OE and control replicates merged) by using bedtools (multicov module) (Quinlan, 2014). Quantile normalization of ATAC-seq data sets was performed with CQN (Hansen et al., 2012), and offsets were fed into DESeq2 to quantify differential accessibility (Love et al., 2014). Nucleosome calling was carried out with NucleoATAC (Schep et al., 2015). Motif enrichment analysis was conducted with HOMER (Heinz et al., 2010) (findMotifsGenome.pl and annotatePeaks.pl). Gene tracks were shown by using the UCSC genome browser. ES cell ATAC-seq data was used from GSM1563569, with reads mapped to the mm10 genome using bowtie2 and analyzed with HOMER (annotatePeaks.pl) and Galaxy/deeptools2 (multiBigwigSummary, plotCorrelation) (Ramirez et al., 2016). NextSeq 500 gds 303504373 GSM3504373 GEO Accession GSM3504373 SRX5101695 GSM3504374 SRP172770 SRS4111937 GSM3504374 RNA-Seq TRANSCRIPTOMIC cDNA RNA from Bead-bound PCM1+ nuclei was collected using the RNEasy Plus Micro kit (Qiagen). Nuclear RNA-seq libraries were constructed with the Stranded RNA-seq Kit with Ribo Erase (Kapa Biosystems) with custom Y-shaped adapters. Paired-end 2x75 bp sequencing was performed for RNA-seq libraries on an Illumina Nextseq instrument (DNA Link). Reads were first mapped to the mouse genome (mm10) using STAR. Differential expression analysis was then carried out with DESeq2. NextSeq 500 gds 303504374 GSM3504374 GEO Accession GSM3504374 SRX5101696 GSM3504375 SRP172770 SRS4111939 GSM3504375 RNA-Seq TRANSCRIPTOMIC cDNA RNA from Bead-bound PCM1+ nuclei was collected using the RNEasy Plus Micro kit (Qiagen). Nuclear RNA-seq libraries were constructed with the Stranded RNA-seq Kit with Ribo Erase (Kapa Biosystems) with custom Y-shaped adapters. Paired-end 2x75 bp sequencing was performed for RNA-seq libraries on an Illumina Nextseq instrument (DNA Link). Reads were first mapped to the mouse genome (mm10) using STAR. Differential expression analysis was then carried out with DESeq2. NextSeq 500 gds 303504375 GSM3504375 GEO Accession GSM3504375 SRX5101697 GSM3504376 SRP172770 SRS4111938 GSM3504376 RNA-Seq TRANSCRIPTOMIC cDNA RNA from Bead-bound PCM1+ nuclei was collected using the RNEasy Plus Micro kit (Qiagen). Nuclear RNA-seq libraries were constructed with the Stranded RNA-seq Kit with Ribo Erase (Kapa Biosystems) with custom Y-shaped adapters. Paired-end 2x75 bp sequencing was performed for RNA-seq libraries on an Illumina Nextseq instrument (DNA Link). Reads were first mapped to the mouse genome (mm10) using STAR. Differential expression analysis was then carried out with DESeq2. NextSeq 500 gds 303504376 GSM3504376 GEO Accession GSM3504376 SRX5101698 GSM3504377 SRP172770 SRS4111940 GSM3504377 RNA-Seq TRANSCRIPTOMIC cDNA RNA from Bead-bound PCM1+ nuclei was collected using the RNEasy Plus Micro kit (Qiagen). Nuclear RNA-seq libraries were constructed with the Stranded RNA-seq Kit with Ribo Erase (Kapa Biosystems) with custom Y-shaped adapters. Paired-end 2x75 bp sequencing was performed for RNA-seq libraries on an Illumina Nextseq instrument (DNA Link). Reads were first mapped to the mouse genome (mm10) using STAR. Differential expression analysis was then carried out with DESeq2. NextSeq 500 gds 303504377 GSM3504377 GEO Accession GSM3504377 SRX5101699 GSM3504378 SRP172770 SRS4111941 GSM3504378 OTHER GENOMIC other Approximately 5 million bead-bound PCM1-enriched cardiomyocyte nuclei, isolated as described above, were used as input for each replicate. The 4C protocol was performed as described previously (van der Werken et al. 2012, Methods in Enzymology), with minor modifications. The first restriction enzyme digestion was performed with DpnII (NEB, R0543M). The first ligation was perfromed overnight with T4 DNA ligase (Roche, 10799009001). Samples were then de-crosslinked with Proteinase K (Thermo Fisher, EO0491) overnight. DNA was purified using P-beads from the NucleoMag 96 PCR kit (Macherey-Nagel, 744100.1). The second enzymatic digestion was performed overnight with Csp6I (Thermo Fisher, ER0211). Samples were then ligated, as described above, overnight and purified with NucleoMag P-beads. We then employed a 2-step PCR protocol to amplify DNA and generate libraries for sequencing. All PCR reactions were carried out with Expand Long template polymerase (Roche, 11681842001). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), at 0.8X. Finally, all libraries were sequenced on an Illumina Nextseq 500. NextSeq 500 gds 303504378 GSM3504378 GEO Accession GSM3504378 SRX5101700 GSM3504379 SRP172770 SRS4111942 GSM3504379 OTHER GENOMIC other Approximately 5 million bead-bound PCM1-enriched cardiomyocyte nuclei, isolated as described above, were used as input for each replicate. The 4C protocol was performed as described previously (van der Werken et al. 2012, Methods in Enzymology), with minor modifications. The first restriction enzyme digestion was performed with DpnII (NEB, R0543M). The first ligation was perfromed overnight with T4 DNA ligase (Roche, 10799009001). Samples were then de-crosslinked with Proteinase K (Thermo Fisher, EO0491) overnight. DNA was purified using P-beads from the NucleoMag 96 PCR kit (Macherey-Nagel, 744100.1). The second enzymatic digestion was performed overnight with Csp6I (Thermo Fisher, ER0211). Samples were then ligated, as described above, overnight and purified with NucleoMag P-beads. We then employed a 2-step PCR protocol to amplify DNA and generate libraries for sequencing. All PCR reactions were carried out with Expand Long template polymerase (Roche, 11681842001). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), at 0.8X. Finally, all libraries were sequenced on an Illumina Nextseq 500. NextSeq 500 gds 303504379 GSM3504379 GEO Accession GSM3504379 SRX5101701 GSM3504380 SRP172770 SRS4111943 GSM3504380 OTHER GENOMIC other Approximately 5 million bead-bound PCM1-enriched cardiomyocyte nuclei, isolated as described above, were used as input for each replicate. The 4C protocol was performed as described previously (van der Werken et al. 2012, Methods in Enzymology), with minor modifications. The first restriction enzyme digestion was performed with DpnII (NEB, R0543M). The first ligation was perfromed overnight with T4 DNA ligase (Roche, 10799009001). Samples were then de-crosslinked with Proteinase K (Thermo Fisher, EO0491) overnight. DNA was purified using P-beads from the NucleoMag 96 PCR kit (Macherey-Nagel, 744100.1). The second enzymatic digestion was performed overnight with Csp6I (Thermo Fisher, ER0211). Samples were then ligated, as described above, overnight and purified with NucleoMag P-beads. We then employed a 2-step PCR protocol to amplify DNA and generate libraries for sequencing. All PCR reactions were carried out with Expand Long template polymerase (Roche, 11681842001). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), at 0.8X. Finally, all libraries were sequenced on an Illumina Nextseq 500. NextSeq 500 gds 303504380 GSM3504380 GEO Accession GSM3504380 SRX5101702 GSM3504381 SRP172770 SRS4111944 GSM3504381 OTHER GENOMIC other Approximately 5 million bead-bound PCM1-enriched cardiomyocyte nuclei, isolated as described above, were used as input for each replicate. The 4C protocol was performed as described previously (van der Werken et al. 2012, Methods in Enzymology), with minor modifications. The first restriction enzyme digestion was performed with DpnII (NEB, R0543M). The first ligation was perfromed overnight with T4 DNA ligase (Roche, 10799009001). Samples were then de-crosslinked with Proteinase K (Thermo Fisher, EO0491) overnight. DNA was purified using P-beads from the NucleoMag 96 PCR kit (Macherey-Nagel, 744100.1). The second enzymatic digestion was performed overnight with Csp6I (Thermo Fisher, ER0211). Samples were then ligated, as described above, overnight and purified with NucleoMag P-beads. We then employed a 2-step PCR protocol to amplify DNA and generate libraries for sequencing. All PCR reactions were carried out with Expand Long template polymerase (Roche, 11681842001). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), at 0.8X. Finally, all libraries were sequenced on an Illumina Nextseq 500. NextSeq 500 gds 303504381 GSM3504381 GEO Accession GSM3504381