SRX4295843 GSM3215429 SRP151293 SRS3458838 GSM3215429 RNA-Seq TRANSCRIPTOMIC cDNA The whole aorta (including the aortic sinus, arch, thoracic aorta and abdominal aorta) was carefully isolated, and the perivascular fat was removed. To remove the adventitia, the whole aorta was incubated with collagenase II (400U/ml) with hyaluronidase (90 U/ml) at 37°C for 8 min, and then the adventitia was physically removed. The aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live foamy and non-foamy macrophages (PI-BODIPY493/503hiSSChiCD64+CD11b+, PI-BODIPY493/503loSSCloCD64+CD11b+) were sorted out using flow cytometry (BD FACSAria III). The sorted cells were quickly added to single cell lysis buffer. The cDNA libraries were prepared from cell lysates in 10X Single-Cell Lysis Buffer (Takara-Clontech) containing 5% RNase inhibitor. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per the manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator with the following parameters: duty cycle, 10; intensity, 5; cycles/burst, 200; and time, 180 seconds. The cDNAs were blunt ended, supplemented with an A base at the 3' end, and then ligated with Illumina sequencing adapters. The ligated fragments were amplified for 12 cycles using primers that incorporated unique index tags. The amplified fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases. Illumina HiSeq 3000 gds 303215429 GSM3215429 GEO Accession GSM3215429 SRX4295844 GSM3215430 SRP151293 SRS3458840 GSM3215430 RNA-Seq TRANSCRIPTOMIC cDNA The whole aorta (including the aortic sinus, arch, thoracic aorta and abdominal aorta) was carefully isolated, and the perivascular fat was removed. To remove the adventitia, the whole aorta was incubated with collagenase II (400U/ml) with hyaluronidase (90 U/ml) at 37°C for 8 min, and then the adventitia was physically removed. The aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live foamy and non-foamy macrophages (PI-BODIPY493/503hiSSChiCD64+CD11b+, PI-BODIPY493/503loSSCloCD64+CD11b+) were sorted out using flow cytometry (BD FACSAria III). The sorted cells were quickly added to single cell lysis buffer. The cDNA libraries were prepared from cell lysates in 10X Single-Cell Lysis Buffer (Takara-Clontech) containing 5% RNase inhibitor. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per the manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator with the following parameters: duty cycle, 10; intensity, 5; cycles/burst, 200; and time, 180 seconds. The cDNAs were blunt ended, supplemented with an A base at the 3' end, and then ligated with Illumina sequencing adapters. The ligated fragments were amplified for 12 cycles using primers that incorporated unique index tags. The amplified fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases. Illumina HiSeq 3000 gds 303215430 GSM3215430 GEO Accession GSM3215430 SRX4295845 GSM3215431 SRP151293 SRS3458844 GSM3215431 RNA-Seq TRANSCRIPTOMIC cDNA The whole aorta (including the aortic sinus, arch, thoracic aorta and abdominal aorta) was carefully isolated, and the perivascular fat was removed. To remove the adventitia, the whole aorta was incubated with collagenase II (400U/ml) with hyaluronidase (90 U/ml) at 37°C for 8 min, and then the adventitia was physically removed. The aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live foamy and non-foamy macrophages (PI-BODIPY493/503hiSSChiCD64+CD11b+, PI-BODIPY493/503loSSCloCD64+CD11b+) were sorted out using flow cytometry (BD FACSAria III). The sorted cells were quickly added to single cell lysis buffer. The cDNA libraries were prepared from cell lysates in 10X Single-Cell Lysis Buffer (Takara-Clontech) containing 5% RNase inhibitor. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per the manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator with the following parameters: duty cycle, 10; intensity, 5; cycles/burst, 200; and time, 180 seconds. The cDNAs were blunt ended, supplemented with an A base at the 3' end, and then ligated with Illumina sequencing adapters. The ligated fragments were amplified for 12 cycles using primers that incorporated unique index tags. The amplified fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases. Illumina HiSeq 3000 gds 303215431 GSM3215431 GEO Accession GSM3215431 SRX4295846 GSM3215432 SRP151293 SRS3458839 GSM3215432 RNA-Seq TRANSCRIPTOMIC cDNA The whole aorta (including the aortic sinus, arch, thoracic aorta and abdominal aorta) was carefully isolated, and the perivascular fat was removed. To remove the adventitia, the whole aorta was incubated with collagenase II (400U/ml) with hyaluronidase (90 U/ml) at 37°C for 8 min, and then the adventitia was physically removed. The aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live foamy and non-foamy macrophages (PI-BODIPY493/503hiSSChiCD64+CD11b+, PI-BODIPY493/503loSSCloCD64+CD11b+) were sorted out using flow cytometry (BD FACSAria III). The sorted cells were quickly added to single cell lysis buffer. The cDNA libraries were prepared from cell lysates in 10X Single-Cell Lysis Buffer (Takara-Clontech) containing 5% RNase inhibitor. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per the manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator with the following parameters: duty cycle, 10; intensity, 5; cycles/burst, 200; and time, 180 seconds. The cDNAs were blunt ended, supplemented with an A base at the 3' end, and then ligated with Illumina sequencing adapters. The ligated fragments were amplified for 12 cycles using primers that incorporated unique index tags. The amplified fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases. Illumina HiSeq 3000 gds 303215432 GSM3215432 GEO Accession GSM3215432 SRX4295847 GSM3215433 SRP151293 SRS3458843 GSM3215433 RNA-Seq TRANSCRIPTOMIC cDNA The whole aorta (including the aortic sinus, arch, thoracic aorta and abdominal aorta) was carefully isolated, and the perivascular fat was removed. To remove the adventitia, the whole aorta was incubated with collagenase II (400U/ml) with hyaluronidase (90 U/ml) at 37°C for 8 min, and then the adventitia was physically removed. The aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live foamy and non-foamy macrophages (PI-BODIPY493/503hiSSChiCD64+CD11b+, PI-BODIPY493/503loSSCloCD64+CD11b+) were sorted out using flow cytometry (BD FACSAria III). The sorted cells were quickly added to single cell lysis buffer. The cDNA libraries were prepared from cell lysates in 10X Single-Cell Lysis Buffer (Takara-Clontech) containing 5% RNase inhibitor. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per the manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator with the following parameters: duty cycle, 10; intensity, 5; cycles/burst, 200; and time, 180 seconds. The cDNAs were blunt ended, supplemented with an A base at the 3' end, and then ligated with Illumina sequencing adapters. The ligated fragments were amplified for 12 cycles using primers that incorporated unique index tags. The amplified fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases. Illumina HiSeq 3000 gds 303215433 GSM3215433 GEO Accession GSM3215433 SRX4295848 GSM3215434 SRP151293 SRS3458841 GSM3215434 RNA-Seq TRANSCRIPTOMIC cDNA The whole aorta (including the aortic sinus, arch, thoracic aorta and abdominal aorta) was carefully isolated, and the perivascular fat was removed. To remove the adventitia, the whole aorta was incubated with collagenase II (400U/ml) with hyaluronidase (90 U/ml) at 37°C for 8 min, and then the adventitia was physically removed. The aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live foamy and non-foamy macrophages (PI-BODIPY493/503hiSSChiCD64+CD11b+, PI-BODIPY493/503loSSCloCD64+CD11b+) were sorted out using flow cytometry (BD FACSAria III). The sorted cells were quickly added to single cell lysis buffer. The cDNA libraries were prepared from cell lysates in 10X Single-Cell Lysis Buffer (Takara-Clontech) containing 5% RNase inhibitor. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per the manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator with the following parameters: duty cycle, 10; intensity, 5; cycles/burst, 200; and time, 180 seconds. The cDNAs were blunt ended, supplemented with an A base at the 3' end, and then ligated with Illumina sequencing adapters. The ligated fragments were amplified for 12 cycles using primers that incorporated unique index tags. The amplified fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases. Illumina HiSeq 3000 gds 303215434 GSM3215434 GEO Accession GSM3215434