- Genomics and Computational Core (Kraus - PI) State-of-the-art genomic technologies combined with cutting-edge computational tools have dramatically advanced our understanding of signal-regulated gene transcription in a wide variety of biological systems. Next generation sequencing-based assays, such as RNA sequencing (RNA-seq), global run-on sequencing (GRO-seq), and chromatin immunoprecipitation sequencing (ChIP-seq), have revealed new information about the regulation of steady-state RNA levels, as well as the localization and regulation of actively transcribing RNA polymerase, transcription factors, and histone modifications across the genome. The global views generated by these assays provide a uniquely informative perspective that cannot be achieved by analyzing one or a few genes at a time. Although the field of reproductive biology has begun to incorporate genomic tools into its repertoire, it has yet to maximize the use of these unique discovery and analysis tools. The goal of this project is to establish a Genomics and Computational Core (GCC) that will serve the needs of all four research projects, all of which propose to use genomic approaches as discovery tools and as assays to probe molecular mechanisms. The GCC will eliminate the need for each lab to establish these methodologies on its own, or to use fee-for-service alternatives that typically only provide first pass data analysis and do not see the experiment through from start to finish. In this regard, the GCC will provide comprehensive service that includes experimental design, genomic library preparation, data analysis, and data archiving. In addition, the GCC will act to promote and facilitate collaborations between the personnel working in different labs. To save costs and increase efficiency, the GCC will leverage infrastructure and expertise already present in the Green Center for Reproductive Biology Sciences. Specifically, the GCC will (1) provide consultation to the PIs and their laboratories during the planning and design stages of all genomic experiments, (2) prepare high-quality genomic libraries from samples collected by the PIs and their laboratories for next generation sequencing, (3) perform quality control analyses on the genomic libraries and the resulting data, and (4) analyze the genomic data generated by the PIs and their laboratories. We anticipate that the GCC will greatly enhance (1) the ease of performing genomic experiments, (2) the quality of the data obtained and the analyses performed, and (3) the efficiency of doing genomic experiments and concomitant waste reduction. Most importantly, the GCC will greatly enhance the efforts of the PIs and their laboratories in obtaining meaningful biological information from genomic experiments.
/ Relevance - Genomics and Computational Core (Kraus - PI) Basic, clinical, and translational studies of the myometrium and cervix during gestation and at term hold great promise for developing new clinical approaches and therapeutic interventions to prevent premature delivery and prolonged labor. State-of-the-art genomic technologies combined with cutting-edge computational tools will aid studies of the myometrium and cervix, yielding new types of information that will greatly advance our understanding of the biology of these tissues.
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|Manders, Dustin B; Kishore, Hari Annavarapu; Gazdar, Adi F et al. (2018) Dysregulation of fibulin-5 and matrix metalloproteases in epithelial ovarian cancer. Oncotarget 9:14251-14267|
|Babayev, Samir N; Kanchwala, Mohammed; Xing, Chao et al. (2018) Thrombin Alters Human Endometrial Stromal Cell Differentiation During Decidualization. Reprod Sci :1933719118768705|
|Mendelson, Carole R; Montalbano, Alina P; Gao, Lu (2017) Fetal-to-maternal signaling in the timing of birth. J Steroid Biochem Mol Biol 170:19-27|
|Kishore, Annavarapu Hari; Liang, Hanquan; Kanchwala, Mohammed et al. (2017) Prostaglandin dehydrogenase is a target for successful induction of cervical ripening. Proc Natl Acad Sci U S A 114:E6427-E6436|
|Babayev, Samir N; Park, Chan Woo; Keller, Patrick W et al. (2017) Androgens Upregulate Endometrial Epithelial Progesterone Receptor Expression: Potential Implications for Endometriosis. Reprod Sci 24:1454-1461|
|Chen, Chien-Cheng; Montalbano, Alina P; Hussain, Imran et al. (2017) The transcriptional repressor GATAD2B mediates progesterone receptor suppression of myometrial contractile gene expression. J Biol Chem 292:12560-12576|
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