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Background  Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine disorder in women of reproductive age and is commonly complicated by adverse endometrial outcomes. Long non-coding RNAs (lncRNAs) are a class of non-protein-coding transcripts that are more than 200 nucleotides in length. Accumulating evidence indicates that lncRNAs are involved in the development of various human diseases. Among these lncRNAs, lncRNA CD36–005 (CD36–005) is indicated to be associated with the pathogenesis of PCOS. However, the mechanisms of action of CD36–005 have not yet been elucidated.    Methods  This study determined the CD36–005 expression level in the uteri of PCOS rat model and its effect on the proliferation activity of rat primary endometrial stromal cells. RNA sequencing (RNA-seq) and bioinformatics analysis were performed to detect the mRNA expression profiles and the biological pathways in which these differentially expressed mRNAs involved, after CD36–005 overexpression in the primary endometrial stromal cells. The differential expression of Hmgn5, Nr5a2, Dll4, Entpd1, Fam50a, and Brms1 were further validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR).    Results  CD36–005 is highly expressed in the uteri of PCOS rat model and promotes the proliferation of rat primary endometrial stromal cells. A total of fifty-five mRNAs differentially expressed were identified in CD36–005 overexpressed stromal cells. Further analyses identified that these differentially expressed mRNAs participate in many biological processes and are associated with various human diseases. The results of qRT-PCR validation were consistent with the RNA-seq data.    Conclusions  These data provide a list of potential target mRNA genes of CD36–005 in endometrial stromal cells and laid a foundation for further studies on the molecular function and mechanism of CD36–005 in the endometrium.    Electronic supplementary material  The online version of this article (10.1186/s12958-018-0412-4) contains supplementary material, which is available to authorized users.

Identification of mRNAs related to endometrium function regulated by lncRNA CD36–005 in rat endometrial stromal cells