Project description:miRNA profiling was carried out using the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno) miRNA were profiled in amygdala brain tissue obtained from adult mice 30 mins after auditory fear conditioning and expression levels compared to tissue obtained from Home cage controls Adult male mice were fear conditioned using tone-shock pairings and brains were harvested 30 mins later. The brains of Home Cage controls and Fear Conditioned animals (n = 4/group) were then punched to collect amygdala tissue. miRNA were extracted using the Qiagen miRNeasy Kit, and then shipped to Exiqon. Exiqon performed labeling, hybridization and data analysis after use of the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno). https://www.exiqon.com/ls/Documents/Scientific/miRCURY-LNA-microRNA-Array-6th-gen-hsa-mmu-rno-manual.pdf
Project description:Mature B-cell differentiation provides an important mechanism for the acquisition of adaptive immunity. Malignancies derived from mature B-cells constitute the majority of leukemias and lymphomas. These malignancies often maintain the characteristics of the normal B-cells that they are derived from, a feature that is frequently used in their diagnosis. The role of microRNAs in mature B-cells is largely unknown. Through concomitant microRNA and mRNA-profiling, we demonstrate a potential regulatory role for microRNAs at every stage of the mature B-cell differentiation process. Further, we have experimentally identified a direct role for the microRNA-regulation of key transcription factors in B-cell differentiation: LMO2 and PRDM1 (Blimp1). We also profiled microRNA of B-cell tumors derived from diffuse large B cell lymphoma, Burkitt lymphoma and chronic lymphocytic leukemia. We found that in contrast to many other malignancies, common B-cell malignancies do not down-regulate microRNAs, but rather maintain the microRNA-expression patterns of their normal B-cell counterparts. Further, each tumor-type maintained the expression of the lineage-specific microRNAs and expression of these lineage-specific microRNAs could correctly predict the lineage of B-cell malignancies in over 90% of the cases. Thus, our data demonstrate that microRNAs may be important in maintaining the mature B-cell phenotype in normal and malignant B-cells. Burkitt lymphoma, Chronic Lymphocytic Leukemia (Mutated), Chronic Lymphocytic Leukemia (Unmutated), Activated B cell-like Diffuse large B cell lymphoma, and Germinal Center-like Diffuse large B cell lymphoma Samples,
Project description:We compared repeatability and comparability of microRNA microarray using 5 different platforms. and compared microarray data generated from five different microRNA microarray platforms with quantitative RT-PCR. Our data suggested that the most accurate and repeatable methods for microRNA expression profiling are Agilent and Toray, and the numbers of detected microRNA at Toray are more than at Agilent. Keywords: repeatability, comparability, microRNA, microarray We compared repeatability and comparability of microRNA microarray using 5 different platforms (Agilent, Ambion, Exiqon, Invitrogen, and Toray). In addition, we compared microarray data generated from five different microRNA microarray platforms with quantitative RT-PCR.
Project description:Amyotrophic lateral sclerosis (ALS) is a paralytic degenerative disease of the nervous system. In the SOD1 mouse model of ALS we found loss of the molecular and functional microglia signature associated with pronounced expression of miR-155 in SOD1 mice. We also found increased expression of miR-155 in the spinal cord of ALS subjects. Genetic ablation of miR-155 increased survival in SOD1 mice and reversed the abnormal microglial and monocyte molecular signature. In addition, dysregulated proteins in the spinal cord of SOD1 mice that we identified in human ALS spinal cords and CSF were restored in SOD1G93A/miR155-/- mice. Treatment of SOD1 mice with anti-miR-155 SOD1 mice injected systemically or into the cerebrospinal fluid prolonged survival and restored the microglial unique genetic and microRNA profiles. Our findings provide a new avenue for immune based therapy of ALS by targeting miR-155. Overall design: Total RNA was isolated from FACS sorted adult FCRLS+ microglia from spinal cords of Non-Tg and SOD1G93A mice from 30d, 60d, 90d, 120d and 140d of age. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. nCounter Nansotring custom-made MG400 chip was used for gene expression profile
Project description:Purpose: The goals of this study are to compare microRNA profiling in different adipose tissues and muscles using microRNA arrays. Methods: Tissue microRNA profiles of 2-3-month old mice were generated by using miRCURY™ LNA microRNA Array. The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission. Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been calculated the median. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data = (Foreground-Background) / median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction. Results and conclusion: The miRNA expression profiling was completed on our samples. The profiling identified a subset of the total number of miRNAs analyzed by the miRCURY™ array that are differentially expressed in brown adipose tissue, inguinal adipose tissue, epidydimal adipose tissue, gastrocnemius muscle, and soleus muscle. Tissue microRNA profiles of 2-3-month old mice were generated by microarray, using miRCURY™ LNA Array.
Project description:Gata6 regulates lung epithelial stem cell development and airway regeneration. Here, the expression profile of microRNA was investigated when Gata6 was depleted during lung development. Analysis used total RNA from Sftpc-rtTA:tetO-cre lungs at E14.5 as control samples (WT) for comparison to the experimental samples of total RNA from Gata6flox/flox: Sftpc-rtTA: tetO-Cre mutant lungs at E14.5.
Project description:Host-virus interaction was analyzed at microRNA expression level. The hypothesis tested in the present study was that rabies virus (RABV) infection affects the microRNA expression in brains of mice and RABV with different virulence induce distinct microRNA expression pattern in host. Results provide important information that RABV infection led to alteration of microRNA expression in brains of mice and FJDRV, a street rabies virus with highly virulence isolated from brain of rabid dog in Fujian provice of China, or ERA, a laboratory-adapted rabies virus with lower virulence induced different microRNA expression pattern, and some them may involved in host defense and immune-related function. An nine chip study was performed using total RNA isolated from brains in Treatment 1, three BALB/c mice infected with FJDRV, Treatment 2, three BALB/c mice infected with ERA, and Control, three BALB/c mice non-infected.
Project description:Accumulation of genetic and epigenetic changes alters regulation of a web of interconnected genes including miRNAs, which confer hallmark capabilities and characteristic cancer features. In this study, the miRNA and mRNA expression profiles of 126 non-small cell lung cancer specimens were analyzed, with special attention given to the diversity of lung adenocarcinomas. Of those, 76 adenocarcinomas were classified into two major subtypes, developing lung-like and adult lung-like, based on their distinctive miRNA expression profiles resembling those of either developing or adult lungs, respectively. A systems biology-based approach using a Bayesian network and nonparametric regression was employed to estimate the gene regulatory circuitry functioning in patient tumors in order to identify subnetworks enriched for genes with differential expression between the two major subtypes. miR-30d and miR-195, identified as hub genes in such subnetworks, had lower levels of expression in the developing lung-like subtype, while introduction of miR-30d or miR-195 into the lung cancer cell lines evoked shifts of mRNA expression profiles towards the adult lung-like subtype. Conversely, the influence of miR-30d and miR-195 was significantly different between the developing lung- and adult lung-like subtypes in our analysis of the patient dataset. In addition, RRM2, a child gene of the miR-30d-centered subnetwork, was found to be a direct target of miR-30d. Together, our findings reveal the existence of two miRNA expression profile-defined lung adenocarcinoma subtypes with distinctive clinicopathologic features and also suggest the usefulness of a systems biology-based approach to gain insight into the altered regulatory circuitry involved in cancer development. Microarray analysis was conducted to examine miRNA expression profiles using a Human miRNA Microarray, pre-commercial version 6.0 (Agilent) with 470 miRNA probes, according to the manufacturer’s instructions
Project description:MicroRNA transcriptional profiling of male Sprague-Dawley rats rat brains comparing microRNA abundance in five different brain regions. Two-condition experiment, regional brain samples vs. universal brain reference. Biological replicates: 4 samples from each region. One sample per array. Each array is divided into 3 replicate subarrays.