SRX2035788 GSM2285553 SRP082420 SRS1629670 GSM2285553 OTHER GENOMIC other Cells were cross-linked with formaldehyde and lysed in cold lysis buffer with nuclei intact as described previously (Nagano et al., 2013; Rao et al., 2014). The chromatin was solubilized with SDS and the accessible chromatin was digested with HindIII. Digested chromatin ends were filled with dNTP mix containing biotinylated dCTP. Nuclear ligation was performed by T4 DNA ligase and DNA-protein cross links were reversed by proteinase K treatment. DNA was purified by phenol:chloroform extraction followed by ethanol precipitation. The biotin-labeled nucleotides at unligated ends were selectively removed by T4 DNA polymerase. Purified DNA was sheared to 300-500 bp and end-repaired using a reaction mix containing T4 DNA polymerase, T4 ploynucleotide kinase and Klenow DNA polymerase. Then the biotinylated ligation junctions were enriched with streptavidin beads. During library preparation, to avoid self-ligation of DNA fragments and to facilitate complementary 5’ overhang (‘T’) ligation of adaptors, a single ‘A’ nucleotide was added to 3’ends of the blunt fragments by using klenow exo-. Adapter ligated DNA fragments were selectively PCR amplified with Illumina primers for 15 cycles and fragments of 400-550 bp were purified using MinElute gel extraction kit (Qaigen). Finally the in situ Hi-C libraries were subjected to paired-end high-throughput sequencing on HiSeq 1000 (Illumina) according to the manufacturer’s protocols. Illumina HiSeq 1000 gds 302285553 GEO Accession GSM2285553 SRX2035789 GSM2285554 SRP082420 SRS1629671 GSM2285554 OTHER GENOMIC other Cells were cross-linked with formaldehyde and lysed in cold lysis buffer with nuclei intact as described previously (Nagano et al., 2013; Rao et al., 2014). The chromatin was solubilized with SDS and the accessible chromatin was digested with HindIII. Digested chromatin ends were filled with dNTP mix containing biotinylated dCTP. Nuclear ligation was performed by T4 DNA ligase and DNA-protein cross links were reversed by proteinase K treatment. DNA was purified by phenol:chloroform extraction followed by ethanol precipitation. The biotin-labeled nucleotides at unligated ends were selectively removed by T4 DNA polymerase. Purified DNA was sheared to 300-500 bp and end-repaired using a reaction mix containing T4 DNA polymerase, T4 ploynucleotide kinase and Klenow DNA polymerase. Then the biotinylated ligation junctions were enriched with streptavidin beads. During library preparation, to avoid self-ligation of DNA fragments and to facilitate complementary 5’ overhang (‘T’) ligation of adaptors, a single ‘A’ nucleotide was added to 3’ends of the blunt fragments by using klenow exo-. Adapter ligated DNA fragments were selectively PCR amplified with Illumina primers for 15 cycles and fragments of 400-550 bp were purified using MinElute gel extraction kit (Qaigen). Finally the in situ Hi-C libraries were subjected to paired-end high-throughput sequencing on HiSeq 1000 (Illumina) according to the manufacturer’s protocols. Illumina HiSeq 1000 gds 302285554 GEO Accession GSM2285554 SRX2035790 GSM2285555 SRP082420 SRS1629672 GSM2285555 OTHER GENOMIC other Cells were cross-linked with formaldehyde and lysed in cold lysis buffer with nuclei intact as described previously (Nagano et al., 2013; Rao et al., 2014). The chromatin was solubilized with SDS and the accessible chromatin was digested with HindIII. Digested chromatin ends were filled with dNTP mix containing biotinylated dCTP. Nuclear ligation was performed by T4 DNA ligase and DNA-protein cross links were reversed by proteinase K treatment. DNA was purified by phenol:chloroform extraction followed by ethanol precipitation. The biotin-labeled nucleotides at unligated ends were selectively removed by T4 DNA polymerase. Purified DNA was sheared to 300-500 bp and end-repaired using a reaction mix containing T4 DNA polymerase, T4 ploynucleotide kinase and Klenow DNA polymerase. Then the biotinylated ligation junctions were enriched with streptavidin beads. During library preparation, to avoid self-ligation of DNA fragments and to facilitate complementary 5’ overhang (‘T’) ligation of adaptors, a single ‘A’ nucleotide was added to 3’ends of the blunt fragments by using klenow exo-. Adapter ligated DNA fragments were selectively PCR amplified with Illumina primers for 15 cycles and fragments of 400-550 bp were purified using MinElute gel extraction kit (Qaigen). Finally the in situ Hi-C libraries were subjected to paired-end high-throughput sequencing on HiSeq 1000 (Illumina) according to the manufacturer’s protocols. Illumina HiSeq 1000 gds 302285555 GEO Accession GSM2285555 SRX2035791 GSM2285556 SRP082420 SRS1629673 GSM2285556 OTHER GENOMIC other Cells were cross-linked with formaldehyde and lysed in cold lysis buffer with nuclei intact as described previously (Nagano et al., 2013; Rao et al., 2014). The chromatin was solubilized with SDS and the accessible chromatin was digested with HindIII. Digested chromatin ends were filled with dNTP mix containing biotinylated dCTP. Nuclear ligation was performed by T4 DNA ligase and DNA-protein cross links were reversed by proteinase K treatment. DNA was purified by phenol:chloroform extraction followed by ethanol precipitation. The biotin-labeled nucleotides at unligated ends were selectively removed by T4 DNA polymerase. Purified DNA was sheared to 300-500 bp and end-repaired using a reaction mix containing T4 DNA polymerase, T4 ploynucleotide kinase and Klenow DNA polymerase. Then the biotinylated ligation junctions were enriched with streptavidin beads. During library preparation, to avoid self-ligation of DNA fragments and to facilitate complementary 5’ overhang (‘T’) ligation of adaptors, a single ‘A’ nucleotide was added to 3’ends of the blunt fragments by using klenow exo-. Adapter ligated DNA fragments were selectively PCR amplified with Illumina primers for 15 cycles and fragments of 400-550 bp were purified using MinElute gel extraction kit (Qaigen). Finally the in situ Hi-C libraries were subjected to paired-end high-throughput sequencing on HiSeq 1000 (Illumina) according to the manufacturer’s protocols. Illumina HiSeq 1000 gds 302285556 GEO Accession GSM2285556