Project description:The LH surge induces panoply of events that are essential for ovulation and corpus luteum formation. The transcriptional responses to the LH surge of pre-ovulatory granulosa cells are complex and still poorly understood. In the present study, a genome wide bovine oligo array was used to determine how the gene expression profiles of granulosa cells are modulated by the LH surge. Granulosa cells from three different statuses were used (1) 2 h before the induction of the LH surge, (2) 6 h and (3) 22 h after the LH surge to assess the short and long term effects of this hormone on follicle differentiation. The results obtained were a list of differentially expressed transcripts for each granulosa cell group. To provide a comprehensive understanding of the processes at play, biological annotations were used to reveal the different functions of transcripts, confirming that the LH surge acts in a temporal manner. The pre-LH group is involved in typical tasks such as cell division, development and proliferation, while the short response of the LH surge included features such as response to stimulus, vascularisation and lipid synthesis, which are indicative of cells preparing for ovulation. The late response of granulosa cells revealed terms associated with protein localization and intra-cellular transport corresponding to the future secretion task that will be required for the transformation of granulosa cells into corpus luteum. Overall, results described in this study provide new insights into the different transcriptional steps that granulosa cells go through during ovulation and before luteinization. Three biological granulosa cells samples: 2 h pre-LH vs. 6 h post-LH vs. 22 h post-LH. Biological replicates: 3 with a technical dye-swap replicates (Dy 547 and Dy 647) for each biological replicate. Hybridizations were performed in a loop design for a total a 9 hybridizations.
Project description:We report for the first time movement of Correia Repeat Enclosed Elements, through inversion of the element at its chromosomal location. Analysis of Ion Torrent generated genome sequence data from Neisseria gonorrhoeae strain NCCP11945 passaged for 8 weeks in the laboratory under standard conditions and stress conditions revealed a total of 37 inversions: 24 were exclusively seen in the stressed sample; 7 in the control sample; and the remaining 3 were seen in both samples. These inversions have the capability to alter gene expression in N. gonorrhoeae through the previously determined activities of the sequence features of these elements. In addition, the locations of predicted non-coding RNAs were investigated to identify potential associations with CREE. Associations varied between strains, as did the number of each element identified. The analysis indicates a role for CREE in disrupting ancestral regulatory networks, including non-coding RNAs. RNA-Seq was used to examine expression changes related to Correia repeats in the strain
Project description:In order to determine whether dis-regulation of a genetic pathway could explain the increased apoptosis of parp-2-/- double positive thymocytes, the gene expression profiles in double positive thymocytes derived from wild-type and parp-2-/- mice were analysed using Affymetrix oligonucleotide chips (mouse genome 430 2.0).
Project description:Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. MicroRNAs are small nucleatides that function as regulators of gene expression in almost any biological process. However, few microRNAs are reported to have a role in the pathological process of OPLL. Therefore, we performed high-throughput microRNA sequencing and transcriptome sequencing of primary OPLL and PLL cells in order to decipher the interacting network of microRNAs in OPLL. MRNA and microRNA profiles were done using primary culture cells of human ossification of the posterior longitudinal ligament (OPLL) tissue and normal posterior longitudinal ligament (PLL) tissue.
Project description:Aberrant miRNA expression has been related to the development of human germ cell tumors, but little is known about effect of ELF-EMFs on miRNA expression. ELF-EMFs may epigenetically modify cells, which may account for the adverse effects of ELF-EMFs on the male reproductive system. To identify miRNAs that were differentially expressed between the sham and ELF-EMF exposure groups, we performed an Affymetrix microarray analysis to establish the miRNA expression profiles. Mouse spermatocyte-derived GC-2 cells were intermittently exposed to a 50 Hz ELF-EMF for 72 h (5 min on/10 min off) at magnetic field intensities of 1 mT and 3 mT. miRNA expression was profiled using Affymetrix Mouse Genechip miRNA 3.0 arrays.
Project description:Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. Recently, disorders of metabolism are thought to be the center of many diseases such as OPLL. Advanced glycation end product (AGE) are accumulated in many extracellular matrixes such as ligament fibers, and it can functions as cellular signal through its receptor (RAGE), contributing to various events such as atherosclerosis or oxidative stress. However, its role in OPLL formation is not yet known. Therefore, we performed high-through-put RNA sequencing on primary posterior longitudinal ligament cells treated with different doses of AGEs (1µM, 5µM and negative control), with or without BMP2 (1µM). mRNA profiles of Primary human posterior longitudinal ligament cells stimulated with various stimuli (Control, 1µM AGE-BSA, 5µM AGE-BSA, 1µM AGE-BSA with BMP2, 5µM AGE-BSA with BMP2) were generated by deep sequencing on Ion Proton
Project description:MicroRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. To this purpose, different measurement platforms to determine their RNA abundance levels in biological samples have been developed. In this study, we have systematically compared 12 commercially available microRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from homologous microRNA family members. We developed novel quality metrics in order to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, quantitative performance, and specificity. The results indicate that each method has its strengths and weaknesses, which helps guiding informed selection of a quantitative microRNA gene expression platform in function of particular study goals.
Project description:In this study, we have investigated the effect of lysine-specific demethylase 6B (KDM6B) on gene expression in normal human germinal center (GC) B cells using a non-viral vector-based system. Gene expression was compared between KDM6B-transfected and control vector-transfected GC B cells from three patients. RNA from the MACS-sorted transfected GC B cells was amplified. 10ug of fragmented cRNA was hybridized to HG-U133 Plus 2.0 microarrays. Differentially expressed genes were identified using Affymetrix GCOS pairwise analysis.