Objective Many physiological and pathological conditions,including cyanotic congenital heart diseases (CCHD),are accompanied by chronic hypoxia,which might interfere with the transcription process.However,the transcriptome profile in peripheral blood under hypoxia is still unidentified.The present work aimed to explore the transcriptional profile alteration of peripheral blood in chronic hypoxia.Methods The present study used a chronic hypoxia rat model to simulate the hypoxic state of CCHD patients.Two groups of Sprague-Dawley rats (n =6 per group) were either exposed to hypoxia (10％ O2) or normoxia (21％ O2) for 3 weeks.Body weight was measured weekly.Peripheral blood was collected and total RNA was extracted for RNA-Seq at the end of the hypoxia treatment.After quality assessment,the library was sequenced by the Illumina Hiseq platform.The differentially expressed genes were screened (false discovery rate ＜ 0.05 and fold change ＞ 2).The functional annotation analysis and duster analysis of differentially expressed genes were performed based on the adjusted P-value (padj ＜ 0.05).Results Compared with the control group,the body weight of the rats in the hypoxia group was significantly lowered (P ＜ 0.01).RNA-Seq results showed that the transcriptome patts of the two groups had significant differences.In total,872 genes were identified as differentially expressed.Among all,803 genes were downregulated,while only 69 genes were up-regulated in the hypoxia group.The functional enrichment analysis of the 872 genes showed that multiple biological processes involved,such as porphyrin-containing compound metabolic process,hemoglobin complex and oxygen transporter activity.Conclusions Our study demonstrated the transcriptional profile alteration in peripheral blood of chronic hypoxia rat model.This study provided basic data and directions to further understand the physiological and pathological changes in patients with CCHD.