Association of microRNAs with colon tumor metastases
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Aaron Schetter
PROVIDER: E-GEOD-44121 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Global miRNA expression profiling of human malignancies is gaining popularity in both basic and clinically driven research. But to date, the majority of such analyses have used microarrays and quantitative real-time PCR. With the introduction of digital count technologies, such as next-generation sequencing (NGS) and the NanoString nCounter System, we have at our disposal, many more options. To make effective use of these different platforms, the strengths and pitfalls of several miRNA profiling technologies were assessed, including a microarray platform, NGS technologies and the NanoString nCounter System. These results were compared to gold-standard quantitative real-time PCR. Comparison of non-small cell lung cancer cell lines grown in vitro (n = 5) and in vivo (n = 5) as xenograft models.
2013-10-22 | E-GEOD-51503 | biostudies-arrayexpress
Project description:We compared the expression of microRNAs in primary colon tumors with their paired liver metastases using the Nanostring human microRNA assays version 1 23 microRNAs were found to be differentially expressed between colon primary tumors and their paired metastases
2014-08-01 | GSE44121 | GEO
Project description:Lung cancer is the leading cause of cancer death worldwide. Low-dose computed tomography screening (LDCT) was recently shown to anticipate the time of diagnosis, thus reducing lung cancer mortality. We identifed a serum microRNA signature (the miR-Test) that could identify the optimal target population for LDCT screening. Here, we performed a large-scale validation study of the miR-Test in high-risk individuals enrolled in the Continuous Observation of Smoking Subjects (COSMOS) lung cancer screening program. RT-qPCR of circulating microRNA purified from serum samples. Trizol-LS and miRNEASY Mini kit (Qiagen) were used for miRNA purification. Custom TaqMan® Low Density Array microRNA Custom Panel (Life Technologies) was used to screen serum circulating microRNA.
2016-02-29 | E-GEOD-76462 | biostudies-arrayexpress
Project description:miRNA profiling of human tonsilar B lymphocytes (naïve B cells, centroblasts and memory B cells) and tonsilar T cells, analyzing the 470 human miRNAs present in miRBase V9.1. B cell subpopulations and T cells were purified using specific antibodies, magnetic beads and the AutoMACS system (Miltenyi Biotec) from reactive tonsils obtained from routine tonsilectomies. Informed consents and the Institutional Review Board approval were obtained. Total RNA was extracted from cell pellets using the mirVana™ miRNA Isolation Kit (Ambion), and sent to LC Sciences facility for microarray hybridization using microfluidics technology. FirstChoice® Human Skeletal Muscle Total RNA (Ambion) was used as common reference for all hybridizations. Background substracted and normalized data from each channel was used to calculate log ratios sample/reference. Keywords: miRNA profiling Dual channel experiments using FirstChoice® Human Skeletal Muscle Total RNA (Ambion) as common reference for all hybridizations. Reference was labeled with Cy5 and the lymphocyte extracted RNA with Cy3. Biological replicates: 4 for each B cell subpopulation (centroblasts, naïve and memory B cells) and 3 for T cells, all of them purified from reactive tonsils with specific antibodies and magnetic beads. Microarray hybridization was performed at LC Sciences, using slides containing in situ synthesized oligonucleotides to detect the 470 miRNAs present in miRBase V9.1. Probes hsa-miR-337 and hsa-miR-542-5p were excluded due to systematic dye bias, according to the manufacturer intructions. Background substracted and normalized detectable data was used to calculate log ratios sample/reference. Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix. Normalization was carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
2009-01-27 | E-GEOD-12934 | biostudies-arrayexpress
Project description:miRNA profiling of human Diffuse Large B Cell Lymphoma (DLBCL) cell lines derived from the two main subtypes of this disease: Activated B Cell like (ABC-DLBCL) and Germinal Center B cell like (GCB-DLBCL), analyzing the 711 human miRNAs present in miRBase V10.0. Five ABC-like DLBCL cell lines (RIVA, Oci-Ly3, Oci-Ly10, HBL1 and U2932) and three GCB-like DLBCL cell lines (Oci-Ly7, Oci-Ly19 and SUDHL-6) were cultured in IMDM (Cellgro) with 20% human plasma, 1% penicillin/streptomycin/L-glutamine (Cellgro,) and 0,2% beta mercaptoethanol (Invitrogen). Total RNA was extracted from cell pellets using the mirVana™ miRNA Isolation Kit (Ambion), and sent to LC Sciences facility for microarray hybridization using microfluidics technology. FirstChoice® Human Skeletal Muscle Total RNA (Ambion) was used as common reference for all hybridizations. Background substracted and normalized data from each channel was used to calculate log ratios sample/reference. Keywords: miRNA profiling Dual channel experiments using FirstChoice® Human Skeletal Muscle Total RNA (Ambion) as common reference for all hybridizations. Reference was labeled with Cy5 and the cell line extracted RNA with Cy3. Biological replicates: 5 ABC-DLBCL cell lines and 3 GCB-DLBCL cell lines. Microarray hybridization was performed at LC Sciences, using slides containing in situ synthesized oligonucleotides to detect the 711 miRNAs present in miRBase V10.0. Probes hsa-miR-337 and hsa-miR-542-5p were excluded due to systematic dye bias, according to the manufacturer intructions. Background substracted and normalized detectable data was used to calculate log ratios sample/reference. Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix. Normalization was carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
2009-01-27 | E-GEOD-12933 | biostudies-arrayexpress
Project description:blood miRNA expression in ischemic stroke compared to controls miRNA expression in blood cells from patients with ischemic stroke were compared to controls with vascular risk factors
2014-07-01 | E-GEOD-55937 | biostudies-arrayexpress
Project description:To identify the role of miRNAs in patient bone marrow (BM) and explore the function of these molecules during HCC progression, we employed microarray-based profiling to analyze miRNA expression in the BM of patients with HCC. MicroRNA expression in the BW of HCC patients was measured by using microarray-based profiling. BM cells were separated into 3fraction by cell surface markers as follows: CD45+(macrophage), CD14-/CD45+(lymphocyte) and CD14-/CD45-/EpCAM+(epithelial cell).
2015-08-06 | E-GEOD-71762 | biostudies-arrayexpress
Project description:MicroRNA-offset RNAs (moRs) were first identified in simple chordates and subsequently in mouse and human cells by deep sequencing of short RNAs. MoRs are derived from sequences located immediately adjacent to microRNAs (miRs) in the primary miR (pri-miR). Currently moRs are considered to be simply a by-product of miR biosynthesis that lack biological activity. Here we show for the first time that a moR is biologically active. We now demonstrate that endogenous and over-expressed moR-21 significantly alters gene expression and inhibits the proliferation of vascular smooth muscle cells (VSMC). We report that the "seed region" of moR-21 as well as the "seed match region" in the target gene 3'UTR are indispensable for moR-21-mediated gene down-regulation. We further demonstrated that moR-21-mediated gene repression is Argonaute 2 (Ago2) dependent. In addition, we find that miR-21 and moR-21 may regulate different genes in a given pathway and can oppose each other in regulating certain genes. Taken together, these findings provide the first evidence that microRNA offset RNA regulates gene expression and is biologically active. Small RNAs were harvested from mouse aortic smooth muscle cells (AoSMCs), with three biological replicates, using miReasy kits (Qiagen) according to the manufacturerâ??s instructions. RNA was quantified using a Nanodrop spectrophotometer. Small RNA library construction and illumina HiSeq 75bp single read sequencing were performed at the Yale Center for Genome Analysis. Reads were trimmed to remove adaptor sequences, and inserts longer than 13 bases were mapped to the mouse mm10 genome using Bowtie (with settings â??n 0 -m 5 --best --strata, allowing 0 mismatches and up to 5 genomic loci with a perfect match, {Genome Biol. 2009;10(3):R25, Langmead B, Trapnell C, Pop M, Salzberg SL}). Reads that mapped to within 50 bp of more than one annotated mouse pri-miR (as defined by miRBase {Kozomara A, Griffiths-Jones S. Nucelic Acids Res 2014 42:D68-D73}), were allotted evenly between these locations. Reads that fell entirely within established miRbase 3p or 5p miR coordinates, plus or minus 3 bp, were counted as 3p or 5p miRs, respectively. Reads that fell entirely within the range of 35 bp 3â?? to 3 bp 5â?? of the last base of a 3p miR were counted as 3p moR reads. Those that fell entirely between 3bp 3â?? and 35 bp 5â?? of the first base of a 5p miR were counted as 5p moR reads. On average each library contained 17.4 million qualifying inserts, of which 13.8 million (79.3%) mapped to one of these four regions, indicating that the large majority of inserts represented miR or moR sequences. Reads were divided by the number of million reads mapping to these regions in each library to give normalized reads per million reads (RPMR) values.
2016-06-01 | E-GEOD-75113 | biostudies-arrayexpress
Project description:Pediatric astrocytomas, a leading cause of death associated with cancer, are the most common primary central nervous system tumors found in children. Most studies of these tumors focus on adults, not children. We examined the global protein and microRNAs expression pattern by 2D SDS-PAGE, mass spectrometry (MALDI-TOF) and RT2 miRNA PCR Array System. MicroRNAs analysis revealed for the first time novel microRNAs involved in astrocytomas biology. Interestingly, miR-138 and miR-145 down-regulation appear to be associated with protein over-expression of vimentin and Bax, respectively. In conclusion, our results show that novel proteins and microRNAs altered on pediatric astrocytoma could serve as biomarkers to distinguish between astrocytoma grades. Astrocytoma samples were colected from patients and total RNA isolation (30 mg of tissue) was performed using the TRIzolM-BM-. protocol (Invitrogen, USA) according to the manufacturerM-bM-^@M-2s instructions. Samples were analyzed using SA Biosciences RT2 miRNA PCRArray System to determied the miRNA expression between control samples and tumors RT2 miRNA PCR Array. Eigth tumor samples and two control tissue (including two control tissue replicates) were used as indicated in the sumary. A total of 3ug of RNA from each tumr samples and control tissue were placed in the PCR Array
2013-02-12 | E-GEOD-44280 | biostudies-arrayexpress
Project description:Murine lung miRNAs were profiled by rodent TaqMan OpenArray after flaxseed feeding and/or radiation exposure Lung tissue was obtained 48 hours after radiation or no exposure from three animals each: flaxseed/no radiation, flaxseed/radiation, control diet/no radiation, control diet/radiation. miRNA profiles were determined by OpenArray.
2014-04-29 | E-GEOD-57123 | biostudies-arrayexpress