MicroRNA profiling of mouse developing forebrain primary neuronal cultures
Ontology highlight
ABSTRACT: C57BL/6 mice at 17.5 days of pregnancy were sacrifced and forebrains of embryos were dissected. Cell plating and culture manipulation were done as previously described [E-MEXP-878]. At day 1, day 2, day 4 and day8 of in vitro culture development, total RNA was extracted and miRNAs were profiled on Illumina Sentrix Universal-96 Array Matrix with microRNA Assay Pool designed against mirBase version 9.1.
Project description:C57BL/6 mice at 17.5 days of pregnancy were sacrifced and forebrains of embryos were dissected. Cell plating and culture manipulation were done as previously described [E-MEXP-878]. At day 1, day 2, day 4 and day 8 of in vitro culture development, total RNA was extracted and profiled on Illumina Sentrix BeadChip Array Mouse-WG6 v1.1 microarray platform.
Project description:Biopsies from 24 gastric adenocarcinomas and adjacent normal gastric mucosa were analyzed for from 24 patients following surgical resection of the tumor. Genome-wide DNA methylation profiling of the tumor and matched non-cancerous mucosa was performed and compared to previously performed gene expression, survival and clinicopathological parametres.
Project description:Adipose tissue is a plentiful and easily accessible source of mesenchymal stem cells that have been shown to be multi potent and possibly have immuno suppressive capacity(Zuk, Zhu et al. 2002; McIntosh, Zvonic et al. 2006; Prichard, Reichert et al. 2008). Several studies have identified hypoxia and the molecular effector of reduced oxygen tension, HIF1α to be essential in the differentiation processes, stem cell proliferation and survival as well as in maintenance of stem cell characteristics (Lennon, Edmison et al. 2001; Goda, Ryan et al. 2003; Wang, Fermor et al. 2005; Lin, Lee et al. 2006; Malladi, Xu et al. 2007; Ohnishi, Yasuda et al. 2007). The fact that oxygen has a central role in cell development and metabolism makes the regulation of oxygen tension a valuable tool in the attempt of exploiting stem cells to their full potential. In the current study we investigate the transcriptional changes caused by two weeks of monolayer hypoxic expansion of human adipose tissue derived stem cells (ASCs). Application of the XVivo hypoxic workstation (BioSpherix, Redfield, NY) made it possible to conduct the expansion of six ASC lines at four different hypoxic conditions in parallel covering the range from mild (15% oxygen) to full hypoxic (1% oxygen) conditions. In this comprehensive investigation the Illumina bead microarray platform was employed to give a profound and new insight in the molecular changes effectuated by hypoxic expansion. The findings of this study demonstrate the significance of biologic variation in the transcriptional response to mild hypoxic expansion and display evidence that full hypoxic growth conditions at 1% oxygen tension selects for a more prolific cell population of reduced chondrogenic potential. Keywords: hypoxia response To investigate the transcriptional response to hypoxia, adipose tissue derived stem cells (ASCs) from six female individuals were cultured for 14 days at different oxygen tensions (ambient, 15%, 10%, 5% and 1%). Gene expression levels at each oxygen tension were compared to ambient conditions (Ambient oxygen tension) using Illumina Human-6 v2.0 microarrays.
Project description:Angiogenesis in collagen gel cultures of rat aorta begins with neovessels sprouting from the aortic explant within the first three days of culture. We used microarrays to detail the pattern of gene expression underlying initial 24 hours of growth, prior to the sprouting of visible neovessles, and identified distinct classes of up-regulated genes during this process. Either freshly harvested aortic rings, representing day 0, or collagen gel cultures of rat aorta were grown in serum free medium and used to prepare total RNA.
Project description:Antiviral responses must be regulated to rapidly defend against infection while minimizing inflammatory damage, but the mechanisms for establishing the magnitude of response within an infected cell are not well understood. miRNAs are small non-coding RNAs that negatively regulate protein levels by binding target sequences on their cognate mRNA. We profiled microRNA expression in the lungs of mice infected for 24 h with Influenza A/PR/8/34 to identify microRNAs that may regulate host response to influenza infection. Mice were infected intranasally with 10e5 pfu Influenza A/PR/8/34. Lungs were isolated after 24 hours and total RNA extracted using Trizol. Equivalent quantities of RNA from 3 infected mice were pooled.
Project description:Human pancreatic islets were isolated from pancreas of deceased donors by Ricordi's procedure and cultured in CMRL 1066 medium additioned with human albumin. EVs were isolated from conditioned medium derived from islet culture after isolation. Once isolated, RNA of islets and islet-derived EVs was extracted and analyzed for microRNA expression within 48 hours after isolation.
Project description:We performed systematic comparison of the miRNA expression profiles between FF and macrodissected FFPE tonsillar tumors using the TaqMan Low Density Array system, with the data processed by different software programs and two types of normalization methods.
Project description:Primary brain tumors are classified and treated based on their histological features, however the factors which specify these tumor types remain largely unknown. We demonstrate that the over-expression of HRAS (V12) and MYC alone or in combination directs the development of glioma, CNS PNET, and atypical teratoid/rhabdoid (AT/RT)-like tumors from postnatal murine p53-deficient neural stem/progenitor cells. Microarray analyses were performed to investigate the gene expression profile of the tumor cells generated by the different genetic perturbations. Murine brain tumors were generated by overexpressing different oncogenes in cultured neurosphere cells from the postnatal lateral ventricle wall region (LVW) of Trp53-deficient mice. Neurosphere cultures were established from isolated cells of the generated tumors, which still expressed the transgene/fluorescent marker gene cassette. Total RNA was isolated and used for gene expression analyses using the Affymetrix Gene 1.0 ST array platform.
Project description:In the majority of colorectal cancers (CRC) under clinical suspicion for a hereditary cause, the disease-causing genetic factors are still to be discovered. In order to identify such genetic factors we stringently selected a discovery cohort of 41 CRC index patients with microsatellite-stable tumors. All patients were below 40 years of age at diagnosis and/or exhibited an overt family history. We employed genome-wide copy number profiling using high-resolution SNP-based array CGH on germline DNA, which resulted in the identification of novel copy number variants (CNVs) in 6 patients (15%) encompassing, among others, the cadherin gene CDH18, the bone morphogenetic protein antagonist family gene GREM1, and the breakpoint cluster region gene BCR. In addition, two genomic deletions were encountered encompassing two microRNA genes, hsa-mir-491/KIAA1797 and hsa-mir-646/AK309218. None of these CNVs has previously been reported in relation to CRC predisposition in humans, nor were they encountered in large control cohorts (>1,600 unaffected individuals). Since several of these newly identified candidate genes may be functionally linked to CRC development, our results illustrate the potential of this approach for the identification of novel candidate genes involved in CRC predisposition. Copy number detection was performed using CNAG2.0 software for 250k SNP arrays and using the Affymetrix Genotyping Console v2.1 software for SNP 6.0 arrays, Reference genomes are included in this data set. Germline genomic DNA from 41 patients with early-onset microsatellite stable colorectal cancer was hybridized on Affymetrix Nsp/6.0 SNP-based arrays according to manufacturer's procedures.
Project description:Angiogenesis in cultures of rat aorta begins with neovessels sprouting from the aortic explant within the first three days of culture. We used microarrys to examine the effects of TNF-alpha on gene expression in both fibrin and collagen gels during the first 48 hours or culture. Rat aortic rings were cultured in either collagen or fibrin maticies. Half of the cultures from each matrix group were treated with 10ng/ml recombinant rat TNF-alpha, and half were left untreated. These cultures were used to prepare total RNA