SRX2208962 GSM2334824 SRP090786 SRS1726325 GSM2334824 OTHER GENOMIC other Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer. Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334824 GEO Accession GSM2334824 SRX2208963 GSM2334825 SRP090786 SRS1726327 GSM2334825 OTHER GENOMIC other Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer. Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334825 GEO Accession GSM2334825 SRX2208964 GSM2334826 SRP090786 SRS1726326 GSM2334826 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was collected using the TRIzol® Reagent (Life Technologies) following the manufacturer's instructions. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334826 GEO Accession GSM2334826 SRX2208965 GSM2334827 SRP090786 SRS1726328 GSM2334827 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was collected using the TRIzol® Reagent (Life Technologies) following the manufacturer's instructions. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334827 GEO Accession GSM2334827 SRX2208966 GSM2334828 SRP090786 SRS1726330 GSM2334828 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was collected using the TRIzol® Reagent (Life Technologies) following the manufacturer's instructions. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334828 GEO Accession GSM2334828 SRX2208967 GSM2334829 SRP090786 SRS1726329 GSM2334829 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was collected using the TRIzol® Reagent (Life Technologies) following the manufacturer's instructions. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334829 GEO Accession GSM2334829 SRX2208968 GSM2334830 SRP090786 SRS1726331 GSM2334830 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was collected using the TRIzol® Reagent (Life Technologies) following the manufacturer's instructions. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334830 GEO Accession GSM2334830 SRX2208969 GSM2334831 SRP090786 SRS1726332 GSM2334831 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was collected using the TRIzol® Reagent (Life Technologies) following the manufacturer's instructions. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334831 GEO Accession GSM2334831 SRX2208970 GSM2334832 SRP090786 SRS1726333 GSM2334832 OTHER GENOMIC other Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer. Cross-linked DNA was digested with HindIII, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. Other steps were following in-situ Hi-C protocol (Rao et al., 2014, Cell). Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334832 GEO Accession GSM2334832 SRX2208971 GSM2334833 SRP090786 SRS1726334 GSM2334833 OTHER GENOMIC other Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer. Cross-linked DNA was digested with MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. Other steps were following in-situ Hi-C protocol (Rao et al., 2014, Cell). Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334833 GEO Accession GSM2334833 SRX2208972 GSM2334834 SRP090786 SRS1726335 GSM2334834 OTHER GENOMIC other Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer. Cross-linked DNA was digested with HindIII, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. Other steps were following in-situ Hi-C protocol (Rao et al., 2014, Cell). Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334834 GEO Accession GSM2334834 SRX2208973 GSM2334835 SRP090786 SRS1726336 GSM2334835 OTHER GENOMIC other Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer. Cross-linked DNA was digested with MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. Other steps were following in-situ Hi-C protocol (Rao et al., 2014, Cell). Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Illumina HiSeq 2500 gds 302334835 GEO Accession GSM2334835