ERX324127 E-MTAB-1930:AA 17 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358281 E-MTAB-1930:pig 17_aortic arch AA extract 17 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324128 E-MTAB-1930:DT 12 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358282 E-MTAB-1930:pig 12_descending thoracic DT extract 12 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324129 E-MTAB-1930:DT 5 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358283 E-MTAB-1930:pig 5_descending thoracic DT extract 5 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324130 E-MTAB-1930:AA 12 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358284 E-MTAB-1930:pig 12_aortic arch AA extract 12 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324131 E-MTAB-1930:DT 14 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358285 E-MTAB-1930:pig 14_descending thoracic DT extract 14 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324132 E-MTAB-1930:AA 10 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358286 E-MTAB-1930:pig 10_aortic arch AA extract 10 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324133 E-MTAB-1930:DT 15 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358287 E-MTAB-1930:pig 15_descending thoracic DT extract 15 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324134 E-MTAB-1930:DT 10 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358288 E-MTAB-1930:pig 10_descending thoracic DT extract 10 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324135 E-MTAB-1930:DT 7 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358289 E-MTAB-1930:pig 7_descending thoracic DT extract 7 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324136 E-MTAB-1930:AA 15 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358290 E-MTAB-1930:pig 15_aortic arch AA extract 15 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324137 E-MTAB-1930:AA 5 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358291 E-MTAB-1930:pig 5_aortic arch AA extract 5 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324138 E-MTAB-1930:DT 13 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358292 E-MTAB-1930:pig 13_descending thoracic DT extract 13 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324139 E-MTAB-1930:AA 14 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358293 E-MTAB-1930:pig 14_aortic arch AA extract 14 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324140 E-MTAB-1930:DT 4 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358294 E-MTAB-1930:pig 4_descending thoracic DT extract 4 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324141 E-MTAB-1930:AA 4 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358295 E-MTAB-1930:pig 4_aortic arch AA extract 4 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324142 E-MTAB-1930:AA 2 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358296 E-MTAB-1930:pig 2_aortic arch AA extract 2 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324143 E-MTAB-1930:AA 3 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358297 E-MTAB-1930:pig 3_aortic arch AA extract 3 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324144 E-MTAB-1930:DT 2 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358298 E-MTAB-1930:pig 2_descending thoracic DT extract 2 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324145 E-MTAB-1930:DT 11 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358299 E-MTAB-1930:pig 11_descending thoracic DT extract 11 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324146 E-MTAB-1930:AA 13 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358300 E-MTAB-1930:pig 13_aortic arch AA extract 13 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324147 E-MTAB-1930:DT 17 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358301 E-MTAB-1930:pig 17_descending thoracic DT extract 17 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta ERX324148 E-MTAB-1930:AA 7 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358302 E-MTAB-1930:pig 7_aortic arch AA extract 7 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324149 E-MTAB-1930:AA 11 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358303 E-MTAB-1930:pig 11_aortic arch AA extract 11 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part aortic arch ERX324150 E-MTAB-1930:DT 3 ERP004025 E-MTAB-1930 Epigenomic code in atherosusceptible endothelia: epigenomic regulation of HOX transcription factors by oxidative stress ERS358304 E-MTAB-1930:pig 3_descending thoracic DT extract 3 MeDIP-Seq GENOMIC 5-methylcytidine antibody Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA. Illumina HiSeq 2000 Experimental Factor: organism part descending thoracic aorta