Genome-wide analysis of HIF1A and ARNT binding in N1E115 cells

Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we analyzed HIF1A and ARNT binding by chromatin immunoprecipitation-sequencing. Libraries were made from chromatin-immunoprecipitated DNA isolated from N1E115 cells cultured in the presence of 20% or 4% oxygen (at ambient barometric pressure) using HIF1A and ARNT antibodies and sequenced on Illumina HiSeq 2500 platform. 20%O2_HIF1A_replicate2 and 4%O2_HIF1A_replicate2 as well as their inputs, 20%O2_input5 and 4%O2_input5, were generated by combining reads from two sequencing runs.