title: Oct4-KO/KO
organism: Mus musculus
attributes.tag: source_name
attributes.value: BCA/Arch/region
attributes.tag: cell type
attributes.value: Mixture of cell types (SMC, Epithelial, Macrophage, others)
attributes.tag: strain
attributes.value: C57BL/6
attributes.tag: isolation
attributes.value: Segments of the aorta from the arch to the aortic root and up to the carotid bifurcation isolated from 18 week western diet fed SMC-Oct4+/+, and SMC-Oct4Δ/Δ (n = 15 each group) mice were snap-frozen in liquid nitrogen and then processed for ChIP assays using the Oct4-specific antibody and sequenced using Illumina TruSeq Chip Library Kit. Sequencing reads were aligned to the mouse genome release M21 (GRCm38.p6) using the BOWTIE alignment tool39. These aligned reads were then processed involving removal of duplicate reads and format conversions using the SAMtools40 suite and converted into bam/bai format and loaded in the Integrative Genomics Viewer for visualization. The reads were also converted to BED format and peaks were identified using MACS241 callpeaks function against the mouse genome with a qvalue < 0.05.
attributes.tag: diet
attributes.value: Western Diet